Marc Piscotty / Getty Images file

Najibullah Zazi, seen in 2009 image, was accused of plotting to bomb New York City's subway system.

U.S. intelligence officials said Saturday that National Security Agency surveillance programs have disrupted "dozens" of terrorist plots in the U.S. and more than 20 countries around the world.

The statement about the thwarted plots was cleared for release by U.S. officials late Saturday afternoon after requests by Senate Intelligence Committee chair Sen. Dianne Feinstein that intelligence agency officials release more information about the surveillance programs to show their effectiveness.

In the statement, intelligence officials said that, of the hundreds of millions of records of U.S. phone calls collected under a provision of the Patriot Act, only 300 were "queried" in 2012 for additional information about the callers.

This was done only after officials found there was a "reasonable suspicion" that the person making the call was "associated with specific foreign terrorist organizations," according to a statement cleared for release by U.S. intelligence agencies.

The only example cited of a thwarted terrorism plot was what officials described as a " major Al-Qa'ida directed attack" intended for the U.S. homeland in 2009. After the NSA discovered that al Qaeda terrorists in Pakistan were in contact with an "unknown person" in the U.S. , the agency alerted the FBI, the intelligence community statement said. The bureau then identified the U.S. contact as Colorado-based extremist Najibullah Zazi. 

After getting Zazi's U.S. phone number from the FBI, the NSA ran it against its mass database of U.S phone calls and discovered a "previously unknown" number for a Zazi co-conspirator, Adis Medunjanin.

The FBI then tracked Zazi as he traveled to New York and arrested him. He pleaded guilty in 2010 to a bomb plot aimed at the New York City subway system and was sentenced to life in prison. Medunjanin was also arrested, convicted and sentenced to life in prison. Officials described the plot "as the most serious terrorist threat on US soil since 9/11," according to the intelligence community statement.

The "operational details" of other plots disrupted "must remain secret to allow us to continue to effectively leverage our capabilities in the face of those who still aspire to do great harm to our citizens and allies," the statement said.  

The statement said that both the program for the collection of telephone metadata and a separate one that intercepts the content of phone calls and emails of foreigners suspected of terrorism operate under “strict controls” that protect the civil liberties of Americans. It emphasized that both are overseen and approved by the secret Foreign Intelligence Surveillance Court, or FISC. 

It also revealed for the first time that records of phone calls that are collected must be destroyed within five years. 

The statement made no reference to what critics have charged have been instances of improper interception of emails and phone calls, including an 86-page, Oct. 3, 2011, FISC opinion — the existence of which was disclosed in a recent Freedom of Information Act lawsuit — finding that some surveillance by the intelligence community was conducted under procedures that violated the Fourth Amendment to the Constitution prohibiting “unreasonable” searches and seizures by the government. 

Feinstein's office said the senator would have no comment on the statement on Saturday. 

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flashpoint-intel.com

The issue includes "Message to the American Nation" supposedly written by al Qaeda in the Arabian Peninsula Commander Qassim Ar-Relmy.

A new issue of the al Qaeda-published propaganda magazine Inspire crows about recent terrorist attacks in Boston and the U.K. and urges young Muslims to carry out similar “lone wolf” operations against the West.

An English-language version of the spring 2013 issue of the online publication, obtained Thursday by NBC News, contains multiple articles praising alleged Boston Marathon bombers Tamerlan and Dzhokhar Tsarnaev and one on last week’s gruesome knife slaying of a British soldier in London.

“When one looks at the terrific Boston Marathon operation and its aftermath, including the accusation of the two brothers, Tamerlan and Dzhokhar Tsarnaev, he understands how a single lone jihad operation can force America to stand on one foot and live in a terrified state, full of fear and rare restlessness,” reads one article under the byline Abu Abdillah Almoravid.

Unlike the last edition of the publication in March, which contained bomb-building recipes – including one using a pressure cooker, similar to the devices deployed near the marathon finish line – and other suggested methods for inflicting small-scale terrorism, the new 39-page issue has numerous pieces aimed at the American audience.

A “Letter from the Editor” warns, “Americans, you should understand this simple equation: as you kill you will be killed. The war is yet to cease, it has barely started. Yesterday it was Baghdad, today it is Boston. The question of ‘who and why’ should be kept aside, You should be asking, “Where is next?”

“Leave us with our religion, land and nations and mind your own internal affairs,” warns another titled “Message to the American Nation” and supposedly written by al Qaeda in the Arabian Peninsula Commander Qassim Ar-Relmy. “Save your economy, look after your concerns.”

The articles also contain numerous high-resolution photos showing the carnage at the Boston Marathon finish line after the bombing on April 15 and one showing the blood-covered suspect in the London slaying of British soldier Lee Rigby.

The gleeful tone extends to the tornado that struck Moore, Okla., on May 20, with an article on that disaster saying, “The Oklahoma tornado took lives, destroyed properties, and still nations, Muslims and others alike, celebrated and prayed for more to strike America. They love to see America in calamities!”

Evan Kohlmann, a partner in the security firm Flashpoint Partners and a terrorism analyst for NBC News, said the leak of the new issue of Inspire follows several weeks of cyberattacks against  al Qaeda's online media network by unknown hostile parties, one of whom apparently managed to penetrate the group's network and briefly post a fake issue.

Last week, U.S. Attorney General Eric Holder identified the previous editor of the propaganda organ, Samir Khan, as one of four Americans killed by U.S. drone strikes overseas. 

Mark Schone, an investigative editor for NBC News, contributed to this report.

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AP / The Lowell Sun & Robin Young

Boston Marathon bombing suspects, from left, Tamerlan and Dzhokhar Tsarnaev.

Tamerlan Tsarnaev landed on America's terrorist watch list in 2011. Tamerlan's younger brother, Dzhokhar, now charged in the Boston Marathon bombing case, seems not to have made the list.

Ultimately, Tamerlan's inclusion on the watch list did not lead investigators to detect the April 15 bomb plot that killed three and wounded at least 260 – prompting inevitable questions about why not, and whether "dots" of intelligence and information that could have been connected were not.

America's terrorist watch list is all about connecting dots – and it is certain to be a focal point for future congressional hearings pegged to the Boston case. A key part of the vast counter-terrorism net cast by the federal government after the 9/11 attacks, the watch list is actually at least nine lists drawn from a single government database. Criteria for determining who gets "nominated" for inclusion in that database – and, then, who actually makes it onto an agency's specific list – are tightly guarded secrets.

CSMonitor quiz: How much do you know about terrorism?

What does seem clear, however, is that the spigot opened wide in the past three years, leading to torrential growth in the core terrorism database. Whether those extra mounds of data give investigators a more accurate view of the universe of terrorists, or whether they have the unintended effect of making prospective terrorists harder to find and the dots harder to connect, is a matter of hot debate – and one that the Boston bombing case may well intensify.

"There's absolutely no question that they're just choking on the volume of information, both classified and unclassified, that's going into the system," says Dakota Rudesill, a visiting professor at Georgetown University Law Center who served, during President Obama's first term, as special assistant in the policy, plans, and requirements directorate of the Office of the Director of National Intelligence, which includes the National Counterterrorism Center. "You're taking on this immense challenge with all this data – like finding a particular needle in a haystack of needles."

US officials bridle at inferences that the system is overwhelmed.

"Certainly, the volume has grown, and the list has grown for a number of reasons," says a US counterterrorism official who spoke on background because he is not permitted to speak on the record. "The intelligence is better; the value of sharing information is seen as better by the agencies involved. The watch list is created specifically to be one of the big dot-connectors in the counterterrorism effort – it's among the most sophisticated systems the government has – and it's proven itself to be effective."

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The making of the watch lists

Like a giant digital vacuum, the Terrorist Identities Datamart Environment (TIDE), a highly classified database maintained by the National Counterterrorism Center in McLean, Va., each day sweeps up thousands of names, aliases, birth dates, and other potential terrorist tidbits – known as "derogatory information" – and tries to match them with hundreds of thousands of names, faces, and identifying biometric data also sent in by the Central Intelligence Agency, the State Department, the Federal Bureau of Investigation, and other US agencies.

"TIDE is the granddaddy repository – not a watch list itself, but it feeds the lists," says Mark Randol, a specialist on domestic intelligence and counterterrorism formerly with the Congressional Research Service (CRS). "The whole deal with a watch list is that you need a place where the objective is to see if you can identify, and stop, people you think are terrorists from just coming into the US and disappearing into the woodwork to plot attacks."

As of December, TIDE contained the names of 875,000 individuals (not including aliases), the counterterrorism center reports. Each day, TIDE sends a river of new names to the Terrorism Screening Center, run by the FBI. The screening center combines TIDE's names with those on the FBI's own domestic terrorism list to create the Terrorism Screening Database (TSDB) – America's master terrorist watch list.

Both TIDE and the TSDB have been expanding fast. TIDE grew from 740,000 names in 2011 to 875,000 in 2012 – an 18 percent jump. The TSDB, for its part, jumped 23 percent from 423,000 individuals in May 2010 to 520,000 in October 2012, according to the CRS and the Terrorism Screening Center.

What happens to the identifying information about a known or suspected terrorist after it is put onto the master terrorism list? The FBI's screening center sends that information to four US agencies with primary responsibility for straining out would-be terrorists, which then add it to their own unclassified watch lists.

State Department. Its Consular Lookout and Support System (CLASS) screens passport and visa applicants.

Department of Homeland Security (DHS). It uses the Traveler Enforcement Compliance System (TECS), which flows into the Interagency Border Inspection System and the Automated Targeting System – lists used by the US Customs and Border Protection for border and port security.

FBI. Its National Crime Information Center list is disseminated as a tool for police departments across the United States. The bureau also has its own Guardian database (different from the TSDB), and Tamerlan Tsarnaev was reportedly on it.

Transportation Security Administration. The TSA, part of the DHS, keeps three air-passenger screening lists – "no fly," "selectee," and "secure flight." The no-fly list is one of the most exclusive watch lists, winnowed to those tagged as possible terrorists who are to be blocked from getting on a US-bound flight. The selectee list signals that an air traveler requires extra screening but being on that list does not necessarily prevent that person from boarding. Both lists have about 20,000 names, the Terrorism Screening Center reports. The secure flight list allows expedited boarding for passengers whose prescreened personal information is compared with watch list data.

Actions that lead to a person being nominated to TIDE as a "known or suspected" terrorist include engaging in terrorist activity, preparing or planning an attack, gathering information on targets, raising funds for attacks, and soliciting membership in a terrorist organization. Less-obvious criteria remain cloaked in secrecy, including nominations that come from foreign intelligence agencies. In 2009, the FBI's own inspector general noted some dissatisfaction with the process, saying the bureau "failed to nominate known or suspected terrorists in 15 percent of the cases we reviewed."

Getting off the list has been problematic, too. The inspector general criticized the FBI for being "untimely in its removal of the subjects" from the watch list in 72 percent of cases reviewed. Travelers who are often delayed at airports are not usually on a watch list; rather, their names and personal information are similar to that of someone who is. In 2012, at least 14,000 records were deleted from TIDE or terrorist watch lists after it was determined that the people no longer met the criteria for inclusion, the counterterrorism center says. US residents make up about 1 percent of TSDB listings.

But civil liberties experts are not satisfied.

"We still don't have access to the information we need to allow us to evaluate how well it's working or how many [who should not be on the list] have been able to get off," says Sharon Bradford Franklin, senior counsel at The Constitution Project, a Washington-based civil liberties group.

How Tsarnaev made the watch list

In March 2011, the FBI interviewed Tsarnaev after Russian intelligence services warned that he had become radicalized. By June, the FBI concluded a basic "assessment" without adding derogatory data to his file, The Washington Post reported. His name, however, did remain in the FBI's Guardian database – an internal watch list.

In September, the Russians again sent up a flare about Tsarnaev's radicalization, this time to the CIA. By year's end, his name had been added to TIDE and the TSDB watch list, the Post reported.

Three days before Tsarnaev left for southern Russia, his name popped up in the TECS system. It is not clear why the rising number of red flags – including his travel to a part of Russia where Islamic radicals are active and his online postings of jihadist videos – did not set off alarm bells. Some analysts say they believe that some important details simply didn't make it into the database.

"If they get the Russian tip, and they were also aware of [the] fact he was visiting Russia and jihadist websites, then I'm not altogether convinced the FBI would have said they found nothing on him," Mr. Randol says. "The fact they didn't see a problem means to me they were not aware of these details."

The near miss that changed watch-listing

AFP - Getty Images file

Umar Farouk Abdulmutallab set off a bomb in his underwear aboard a Detroit-bound airliner on Christmas Day 2009. A month before his father had warned U.S. authorities. Abdulmutallab's name was added to TIDE -- but didn't make it onto the watch list.

Connecting dots so that clues are not left floating in a sea of data was a top goal after the near-miss Christmas Day bombing attempt in 2009. Nigerian national Umar Farouk Abdulmutallab famously tried to blow up a Detroit-bound airplane using plastic explosives hidden in his underwear.

On Nov. 18, 2009, Mr. Abdulmutallab's own father reported his son's radicalization to US Embassy officials in Nigeria. A week later, the son's name was added to TIDE, but not to the watch list – in part because the source of the derogatory information was not included, weakening it. Five weeks later, Abdulmutallab tried to blow up the plane.

Afterward, President Obama ordered a review to determine why Abdulmutallab's name had not appeared on the master watch list. Later in 2010, the nominating criteria changed, with the result that more names and data flowed into TIDE and the TSDB. One measure of the increase: The number of US citizens and lawful permanent residents on the no-fly list more than doubled, the Government Accountability Office (GAO) found in a 2012 study of watch list changes.

Even before the changes, concern was evident within the intelligence community about the huge amount of data being funneled into TIDE. Back in March 2010, Russell Travers, then deputy director of information sharing and knowledge development at the National Counterterrorism Center, told a Senate panel that the inflow of 10,000 names a day to TIDE had required some adjustments. Among them was the advent of special "pursuit teams" of analysts to explore threads, threats, and loose ends that would help "connect the dots," he said, acknowledging that the step was "an experiment."

The 2012 GAO report likewise noted concern among "nominating agencies" about their abilities to process so much information – especially after the changes that followed the underwear bombing attempt. It noted that "agencies are ... pursuing staffing, technology, and other solutions to address challenges in processing the volumes of information."

A notable watch list success

U.s. Marshals Service / AP file

Faisal Shahzad, shown in a U.S. Marshal's Service mugshot, got on an airplane for Pakistan after the attempt to set off a car bomb in New York's Times Square. A watch list flagged him, and authorities arrested him on the jet.

Despite the fire hose of incoming information, the US saw some success in apprehending terrorism suspects. After someone tried to set off a car bomb in New York's Times Square on May 1, 2010, investigators traced the crime to Pakistani-American Faisal Shahzad – and added his name to the no-fly list at 12:30 p.m. on May 3. Later that evening, Mr. Shahzad was indeed attempting to make his getaway to Pakistan. Minutes before his flight was to depart, authorities spotted his name during a final check.

"What used to happen in days now happens in minutes or seconds," the US counterterrorism official says of recent watch list updating and technology upgrades. "The Times Square bomber actually got on the plane thinking he was getting away. But we have a real-time transactional interface with the Customs and Border Patrol. They screened the passenger manifest, arrested him, and took him off the plane."

Today, says the US counterterrorism official, the backlog of information has been eliminated and analytical resources are adequate. The number of names on the TSDB fluctuates, but during the past year appears to have "leveled off" at about a half million, he says.

Unconnected 'dots' in Tsarnaev case?

Questions remain, however, about the government's handling of Tsarnaev during the year leading up to the Boston bombings. Some wonder why he was not a candidate for extra scrutiny by a pursuit team or by the FBI. Others ask why federal authorities did not inform local police of the warnings about Tsarnaev's possible radicalization, so they could possibly keep an eye out.

Were there dots that, if connected, would have led to closer FBI scrutiny and prevention of the Boston Marathon bombings? If so, did data overload play a role?

"No, actually more data makes it more effective," insists the counterterrorism official. "The more derogatory information in there, the better able the system is to screen, and the better the whole system works."

But data overload is likely to be raised in future hearings on Capitol Hill, some say.

"I hope the Boston case will lead to a new revision of the watch list, to see whether we are adding just too much information on people so that it leads to a needle-in-the-haystack problem," Randol says.

"Right now, it isn't clear that there are plans in place to review the effectiveness of the watch list or whether the level of misidentification is growing because the haystacks are getting too big."

This report, "Terrorist watch lists: Are they working as they should?," first appeared on CSMonitor.com.

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In the fall of 2011, a key Boston police counterterror intelligence unit -- funded with millions of dollars in U.S. homeland security grants -- was closely monitoring anti-Wall Street demonstrations, including tracking the Facebook pages and websites of the protesters and writing reports on the potential impact on "commercial and financial sector assets" in downtown areas, according to internal police documents.

The police monitoring of the activities of Occupy Boston -- an off-shoot of the Occupy Wall Street protests that swept the country in 2011 -- came during a period after the U.S. government received the second of two warnings from the Russian government about the radical Islamic ties of alleged Boston Marathon bomber Tamerlan Tsarnaev.

Boston Police Commissioner Ed Davis told a congressional panel Thursday that his department was never alerted by any federal agency to the information about Tsarnaev, but added that it was "hard to say" whether it would have made any difference in preventing the bombing. FBI  officials have insisted that the intelligence about Tsarnaev was vague and uncorroborated and that their own assessment at the time produced no "derogatory" information that justified opening a full-scale investigation.

But the internal Boston police documents, recently obtained by a civil liberties group, could raise fresh questions about the role of Homeland Security-funded "fusion centers" like the Boston Regional Intelligence Center, or BRIC, which conducted the monitoring. The Boston unit  is one of 72 such units set up to collect, analyze and share intelligence about potential terror threats. While  Homeland Security Secretary Janet Napolitano has called the units “one of the centerpieces” of the nation’s counterterrorism efforts, congressional critics have questioned their effectiveness and accused them in some cases of writing "useless" reports that infringed on civil liberties.

“They  were monitoring completely lawful activities,” said Mara Verheyden-Hilliard, executive director of the Partnership for Civil Justice, a civil liberties group that recently obtained the documents on the BRIC’s monitoring of Occupy Boston under the Freedom of Information Act. She said the BRIC monitoring was an example of the “vast expenditure of government money” to collect intelligence on activities unrelated to terrorism, in violation of First Amendment rights.

A Boston police spokeswoman said the department has changed its reporting procedures since the monitoring of the protests and emphasized that the BRIC is “about a lot more than terrorism.”

A Homeland Security official declined comment, saying the BRIC, like other fusion centers, was “locally owned and operated.” But the official noted that, just five days before the marathon bombing, the BRIC did produce an assessment for the event that, while concluding there was “no specific” or “credible” threat information, advised that “officials should be aware of a range of potential terrorist threats, from scattered unsophisticated attacks to dispersal of chemical or biological agents.” The assessment also identified the marathon finish line — where the bombing took place — as well as Fenway Park as “an area of increased vulnerability.”

The internal police documents about the activities of the BRIC show that on Sept. 30, 2011 — just two days after the second Russian warning about Tsarnaev was sent to the CIA — the Boston police unit was focused on an upcoming “Take Back Boston Rally” planned for the city’s Dewey Square.

“Approximately 100 people are listed as attending the Take Back Boston Rally on the event’s Facebook page and Occupy Boston organziers are encouraging people to attend it as well,” reads one BRIC report written by a U.S. homeland security official on Sept. 30, 2011. “The BRIC has received information that approximately 700 people will participate in the Take Back Boston march, with approximately 100 people staying to camp out as part of Occupy Boston.”

A follow-up report, three days days later, tracked the number of protesters, noting that “the size of the camp in Dewey Square has steadily grown over the weekend” and that “according to the group’s website” the demonstrators were planning two marches, including one to a “local media station, very likely to be Fox News Boston on Beacon Hill.”

Verheyden-Hilliard, whose group obtained the documents, said it was not surprising that the BRIC would be reporting such information since later documents appear to show Homeland Security officials requesting such data. In one “Daily Intelligence Briefing,” dated Oct. 21, 2011, the “Threat Management Division” of Homeland Security’s Federal Protective Service outlines a “template for creating the daily intelligence brief for your region” and then cites a “list of events we want to request” that officials submit “for daily briefing information.” Among the categories, in addition to reporting on domestic terrorist acts and “significant criminal activity” is one called “Peaceful Activist Demonstrations.”

NBC News

Boston Police Commissioner Ed Davis testifies Thursday before a House committee on the marathon bombings.

In his testimony Thursday, Commissioner Davis acknowledged to a House committee that his department, which runs the BRIC, was never provided any of the intelligence from the FBI and CIA that Tsarnaev, a resident of Cambridge, had been twice flagged by the Russians as an Islamic radical with ties to “underground” groups in that country.

“We were not aware of the two brothers,” Davis said in response to questioning by Rep. Mike McCaul of Texas, chairman of the House Homeland Security Committee. “We were not aware of Tamerlan’s activities.”

Davis acknowledged that police counterterrorism detectives were assigned to an FBI Joint Terrorism Task Force (JTTF) -- a separate unit from the Homeland Security fusion centers that serves as the government's primary investigative arm for probing terror threats. An FBI agent at the Boston JTTF conducted an “assessment” of Tsarnaev in 2011 after the first warning about his ties was sent by Russia’s FSB intelligence service. The assessment found no “derogatory” information about Tsarnaev that justified conducting a formal investigation. Later information about Tsarnaev included a second Russian warning to the CIA on Sept. 28, 2011.

But while Boston police had access to the JTTF’s classified database, Davis said that his own officers assigned to the task force were never  specifically alerted to any the information about Tsarnaev. “They tell me they received no word about that individual prior to the bombing.”

FBI spokesman Jason Pack said Thursday that state and local members of the JTTF are “responsible for maintaining awareness of possible threats” in their areas and could have performed “customized key word searches” of the FBI database that would have yielded the information about Tsarnaev.

NBC News researcher Taylor Sears contributed to this report.

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NEW YORK -- Federal prosecutors on Thursday revealed charges that accuse a Tunisian man who had lived in Canada with applying for a visa "to remain in the United States to facilitate an act of terrorism." 

The charges name Ahmed Abassi, a native of Tunisia who had been living in Canada.  Prosecutors say he came to New York in mid-March. 

Federal investigators say he met with the men involved in a plot -- first revealed in mid-April -- to attack an Amtrak passenger train from New York to Toronto.  They say the plotters discussed blowing up a bridge at Niagara Falls to cause the train to plunge into the gorge below. 

Canadian authorities announced in mid-April that the plot had been stopped. They disclosed then that they had arrested two men -- Chaieb Esseghaier of Montreal, a 30-year-old Tunisian graduate student who is reported to have guerrilla warfare training and is described as the ringleader, and Raed Jaser of Toronto, 35, a school bus driver.

Frank Gunn / AP

Chiheb Esseghaier, one of two suspects arrested last week in Canada in connection with the alleged terror plot to derail a passenger train near the U.S.-Canada border, arrives at Buttonville Airport outside Toronto on April 23.

Federal prosecutors from the Southern District of New York said Thursday that Abassi was arrested 17 days ago. The fact that word of his arrest was withheld indicates he was likely providing some information about the plot to investigators. 

He is charged with fraudulently applying for a work visa "in order to remain in the United States to facilitate an act of international terrorism," according to a statement from the Justice Department. 

Authorities in Canada said in April that an al Qaeda facilitator in Iran had worked with Esseghaier, and also that the train they intended to target was an Amtrak train originating in New York's Penn Station. 

"Esseghaier was simply a bad guy, and dangerous. This guy was purely evil," said one investigator, and had scientific training and the technical ability to make chemical bombs. 

Law enforcement officials say Esseghaier met Abassi during a trip to New York. But they say the meeting did not go well.  Abassi, they say, thought he should be the person in charge. As a result of the failure to get along, Abassi did not have a role in the derailment plot. Authorities did not spell out any further the basis for the visa fraud charge beyond saying it was to facilitate an “act of terror.” 

The FBI has covertly monitored the activities of the two Canadian men, their contact with overseas Al Qaeda facilitators and others, and their possible connection to others who could be linked to the plot. 

"What Mr. Abassi didn't know was that one of his associates, privy to the details of the plan, was an undercover FBI agent," said George Venizelos, the FBI Assistant Director in Charge of the New York office. 

The yearlong covert investigation involved electronic and physical surveillance. Authorities emphasize, however, that this was no sting operation.  It was, they say, a significant terror plot, once which failed to get more notice because of the Boston Marathon bombings. 

CTV News via Reuters

Raed Jaser is seen arriving at court in the back of a police car in Toronto on April 23.

Esseghaier and Jaser made their initial court appearances in Canada in April. They are charged with conspiracy to commit murder, conspiracy to interfere with transportation and participating in terrorist group activities. Esseghaier told the court that the Criminal Code of Canada “is not a holy book” and did not apply to him.

Richard Esposito is senior executive producer of the NBC News investigative unit; Jonathan Dienst is WNBC chief investigative reporter and NBC News contributing correspondent in New York City; Pete Williams is NBC News justice correspondent.

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A badly wounded but awake Dzhokhar Tsarnaev showed little signs of fear or remorse during his hospital room court hearing earlier this week and his heart monitor didn’t register a blip when he was told he was facing the death penalty in the Boston Marathon bombing case, according to a source familiar with the events inside the hospital room when he was read his rights.

Tsarnaev’s face was splotched and swollen, his left hand was bandaged, and he was unable to talk during the brief court hearing presided over by U.S. Judge Marianne Bowler on Monday afternoon.

The surviving bombing suspect mouthed rather than said the word “no” when asked if he could afford a lawyer and nodded in the affirmative when asked if he understood his rights.

But Tsarnaev appeared to fully follow the proceeding, the source said. The most telling moment, the source said, came early on when, after Tsarnaev was informed of the two charges against him, the judge asked prosecutor William Weinreb to spell out the possible penalties he was facing.

“Your honor, the maximum penalty is death,” Weinreb said, according to a public transcript of the proceeding.

Tsarnaev showed no reaction — nor did his heart monitor register any change, the source said. “There was no blip at all,” said the source.

But heart monitors don’t always register emotional responses — and there is no way to tell what impact medications Tsarmaev may have been given had, according to medical experts.

There have also been conflicting reports about Tsarnaev’s mental state in the days after his capture. “Over the weekend, he’s in and out of lucidity,” Rep. Mike Rogers, chairman of the House Intelligence Committee, said on MSNBC’s “Andrea Mitchell” show on Thursday. “He’s got — he’s on medication, he’s talking, but he’s not talking, he’s unconscious, he’s going for medical procedures.”

But those present at the bedside court hearing were convinced that Tsarnaev was fully cognizant of the circumstances he was facing, the source said. Judge Bowler agreed. “I find the defendant is alert, mentally competent and lucid,” she said, according to the transcript. “He is aware of the nature of the proceedings.”

Handout / FBI via Reuters

Dzhokhar Tsarnaev, 19, has been charged in the Boston Marathon bombing.

The court proceeding erupted as a source of controversy Thursday when Rogers charged that Judge Bowler had interfered with FBI questioning of Tsarnaev – and that the Justice Department failed to object — when she ordered that Tsarnaev be read his rights on Monday, a day after he was charged in a then-sealed complaint at 6:47 p.m. Sunday.

FBI agents were questioning Tsarnaev — and getting his responses in writing — under a “public safety exception” that allows agents to obtain information from criminal suspects for 48 hours without reading them their constitutional rights informing them they have the right to remain silent and a right to a lawyer. The information that agents got — including the disclosure Thursday that Tsarnaev and his brother had talked about driving to Times Square to set off more bombs — came during those sessions over the weekend.

But Rogers said Thursday that FBI agents “weren’t quite finished with him” when Bowler directed that the court hearing take place that Monday. “To have the court affirmatively push their way in, is — A) I think it's wrong, and B) we should have given the FBI the time that they needed.” Justice Department officials “have a lot of explaining to do.”

Bowler, asked by NBC News about Rogers’ charges in her federal courtroom in Boston Thursday, replied: “The court does not comment.”

A  federal law enforcement official disputed Rogers’ account, telling NBC News that FBI agents had already left the hospital room and wrapped up their questioning before the court hearing took place mid-day Monday. In a statement emailed to reporters Thursday, Justice Department spokesman Dean Boyd said that, after the criminal complaint was filed, the rules of criminal procedure required the judge to advice the defendant of his rights. 

“The prosecutors and FBI agents in Boston were advised of the scheduled initial appearance in advance of its occurrence,” he said. 

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Cambridge Police Department

Tamerlan Tsarnaev is seen in a booking photo from a 2009 arrest in Cambridge, Mass.

A Homeland Security officer assigned to the FBI's Joint Terrorism Task Force in Boston was alerted by email that Tamerlan Tsarnaev was traveling to Russia in January 2012, according to a U.S. counterterrorism official and a congressional investigator briefed on the investigation.

But the email — sent because Tsarnaev's name was on a Homeland Security watch-listing database — generated no further scrutiny of Tsarnaev. The officer has told officials he receives hundreds of such emails and doesn't remember getting the alert about Tsarnaev's travel to Russia, said the U.S. counterterrorism official who has been briefed on details on the probe. 

Federal officials who have been reviewing the government's handling of Tsarnaev say that it is still not clear that any further steps could have been taken to monitor Tsarnaev's activities. But congressional investigators are now questioning whether there were breakdowns in communications among the agencies — in part because of different spellings used for his name — that prevented officials from piecing together clues and sharing information. 

A government-wide review has found that information about Tsarnaev had been entered into three classified counterterrorism databases: a Guardian file maintained by the FBI on all potential terror suspects, a TECS watch-listing database maintained by Homeland Security and a master TIDE list of potential or suspected terrorists maintained by the National Counterterrorism Center, according to the sources and public statements by U.S. government officials.

But not all the entries were identical, using different spellings and dates of birth that government computer programs failed to match up, said the U.S. official briefed on the probe.

The first entry in the FBI's Guardian file was generated because of the original Russian request in early 2011 reporting that Tamerlan Tsarnaev was a follower of radical Islam with possible connections to "underground" groups. That triggered his entry into the TECS watch listing database and an investigation by the FBI"s Joint Terrorism Task Force — including interviews with Tsarnaev and members of his family. But agents found no negative information and closed the case. The FBI asked the Russians for more details and never got a response.

U.S. officials say that the CIA received its own report from the Russian FSB about Tsarnaev in September 2011 — and entered him into the TIDE terrorism database. Officials say the CIA, using the information it got from the Russians, entered two different spellings of his name and two different dates of birth into the TIDE system.

A U.S. intelligence official said: "The CIA shared all the information provided by the foreign government. including two possible dates of birth, his name and a possible name variant as well. No information was incorrectly entered in the watch listing system, all the information was shared precisely as the foreign government provided it."

But the counterterrorism official briefed on the probe say this may have created confusion because the primary entry was made under a spelling that was different than that used by Tsarnaev — one letter was off — and which had been entered into the FBI's Guardian database.

When Tsarnaev showed up at the airport for his January 2012 trip to Russia, Customs and Border Patrol officers noticed his entry in the TECS system, triggering the email to the CBP agent assigned to the Joint Terrorism Task Force in Boston. But while Tsarnaev was subjected to some extra questioning, agents had no grounds to prevent him from traveling. "It's not like he was going to Yemen or Somalia," said the official briefed on the probe.

By the time Tsaernaev returned, his name had been purged from the TECS watch-listing database because of time limits on how long "U.S. persons" can stay in the database when there is no additional derogatory information, the official said. The FBI also took no further steps to question Tsarnaev about the reasons for his trip or who he met with overseas, officials say. 

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Rich Pedroncelli / ASSOCIATED PRESS

Umer Hayat, left and his son, Hamid, of Lodi, Calif., were convicted in a 2005 terrorism case.

Jihadist websites, with their heroic militaristic videos and messages promising everlasting life to martyrs, have shown themselves capable of inciting would-be holy warriors to action. But an expert on Islamic terrorism says less attention has been paid to another breeding ground for radicalization that is even harder to police – the family dinner table.  

Familial indoctrination and recruitment for terrorism emerged as a theme in a study of 50 high-profile terrorist attacks since 2001 by Karen Greenberg, director of the Center on National Security at Fordham Law School. In at least eight of those cases, radicalization occurred within families, most often involving an “elder-younger relationship,” she said.

"Several terrorism prosecutions in the United States have included fathers and sons, brothers, and even cousins,” Greenberg said. “The importance of this is to underscore the way in which the personal and the political often intersect in these cases -- and also the importance of the effect of an influential often older person or figure in pushing the radicalization along -- extending what might otherwise be a lone-wolf narrative to a slightly larger circle.”

With family members -- and reportedly even Dzhokhar Tsarnaev himself -- telling authorities that his older brother, Tamerlan, encouraged him to embrace radical Islam, the blood-relative scenario may now be playing out in the Boston Marathon bombings.

While Tamerlan Tsarnaev, 26, reportedly was himself led down the radical road by a mysterious man known to family members only as “Misha,” he in turn exerted tremendous influence over younger brother, Dzhokhar, 19,  according to some relatives.

"They all loved Tamerlan. He was the eldest one and he, in many ways, was the role model for his sisters and his brother," Elmirza Khozhugov, 26, the ex-husband of Tamerlan's sister, Ailina, told the Associated Press. "You could always hear his younger brother and sisters say, 'Tamerlan said this,' and 'Tamerlan said that.' Dzhokhar loved him. He would do whatever Tamerlan would say.”

If investigators gather evidence to support that scenario, Dzhokhar Tsarnaev’s defense is likely to play the under-the-influence card in an effort to paint their client in a sympathetic light and, if he is convicted, possibly mitigate what could be a death sentence.

Whatever the outcome, Greenberg said she sees similarities between the Tsarnaev case and eight that preceded it – a list that doesn’t include three sets of Saudi brothers involved in the Sept. 11, 2011, terror attacks on the United States: the al-Ghamdis (Ahmed and Saeed), al-Shehris (Mohand, Wail and Waleed) and al-Haznis (Nawaf and Salem).

Among the other high-profile cases cited by Greenberg, all of which resulted in convictions on material support for terrorism charges at a minimum:

• The 2007 plot to attack the Army’s Fort Dix in New Jersey, in which six radicals planned an attack on the Fort Dix military reservation in New Jersey. The plot, "to kill as many soldiers as possible," including three brothers -- Shain Duka, Eljvir Duka, Dritan Duka – ethnic Albanians who were born in Macedonia. All were sentenced to life in prison for conspiracy to commit terrorism.
• A 2006 Toledo plot which two cousins, Zubair Ahmed and Khaleel Ahmed, and three other men were convicted of plotting to train jihadists in Ohio for eventual missions against U.S. troops in Iraq. They were sentenced to 10 years and eight years and four months in prison, respectively, in 2010.
• The so-called Portland Seven plot, in which Oregon residents and brothers Ahmed and Muhammad Bilal, were among seven militants who traveled to China in hopes of crossing into Afghanistan to fight with the Taliban against U.S. troops. In this case, prosecutors said the older brother, Ahmed, radicalized his younger brother. They received sentences of 10 years and eight years, respectively.

AP

These undated file photos provided by the City County Bureau of Identification in Wake County, N.C., show from left: Daniel Patrick Boyd, Hysen Sherifi, Mohammad Omar Aly Hassan and Ziyad Yaghi. Authorities claim the group and others, including Boyd's sons, were gearing up for a "violent jihad" overseas.

• A 2009 Quantico, Va., plot, in which a father, Daniel Patrick Boyd, and two of his sons, Zakariya and Dylan, were among eight men convicted of plotting “to advance violent jihad, including supporting and participating in terrorist activities abroad and committing acts of murder, kidnapping or maiming persons abroad.” Prosecutors said the men traveled to Gaza, Jordan and Kosovo after training in North Carolina, in an effort to “commit jihad.” The elder Boyd, a convert to Islam, pleaded guilty to conspiracy to kill people overseas and of material support for terrorism and was sentenced to 18 years in prison. Zakariya and Dylan Boyd pleaded guilty to conspiracy to provide material support to terrorism and received sentences of nine and eight years, respectively.
• A 2005 case in Lodi, Calif., in which a father and son, the Hayats were charged with training in Pakistan to commit jihad. The son, Hamid, a 24-year-old cherry packer, was ultimately found guilty of international terrorism and sentenced to a 24-year prison term. His father, Umer, charged with two counts of making false statements to the FBI, ultimately pleaded guilty and was ordered released for time served.

While family ties have lured some into terrorism, some have used their influence to warn family members away from jihad.

Osama bin Laden himself reportedly warned his 24 children not to follow his path.

In a four-page will published by a Kuwaiti newspaper shortly after his death on May 2, 2011, the elder bin Laden tried to justify his terrorist activities against the United States and Israel, but warned his kids against emulating him.

Unfortunately for them, three younger bin Ladens – Khalid, Hamza and Sa’ad – already had entered the family business.

Khalid died with his father in the Navy SEAL raid on their compound in Abbottabad, Pakistan; Saad was killed in a U.S. drone strike in Pakistan in 2009. The whereabouts of Hamza bin Laden, who was reportedly being groomed to be his father’s successor after Saad’s death, are unknown.

Robert Windrem is a fellow at the Center on National Security. 

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The arrest of Dzhokhar Tsarnaev ended the manhunt for the Boston Marathon bombers, but it set in motion an equally intense phase of the case that will begin with the grilling of the man who – for now at least – is the only surviving suspect.

An indication of the complex investigation ahead came Friday night, when an Obama administration official told NBC News that Tsarnaev would not be given a Miranda warning when he is physically able to be interrogated after receiving medical treatment.

Instead, the official said, the government will invoke a legal rule known as the "public safety exception," which will enable investigators to question Tsarnaev without first advising him of his right to remain silent and to be afforded legal counsel.

The exemption can be invoked when information is needed to protect public safety. In this instance, the government believes it's vital to find out if Tsarnaev planted any other explosives before his capture or whether others might have plotted with him to do so, said the official, speaking on condition of anonymity.

Tsarnaev’s older brother, Tamerlan, was killed in a shootout with police early Friday, and it was not clear until late Friday that authorities would be able to question their remaining prime suspect.

Until shortly before his capture around 8:45 p.m. ET, the wounded and bleeding Tsarnaev exchanged gunfire with authorities in Watertown, Mass., while sheltering in a plastic-wrapped pleasure boat.

Officers on the scene and the brass in the command center were both clearly elated by the outcome.

“We always want to take someone alive so we can find out what happened,” Boston Police Commissioner Ed Davis said at a media briefing an hour later, “and we can hold them to justice."

High Value Detainee Interrogation Group
The rule waiving the Miranda warning does not set a precise limit on how long a suspect can be interrogated before being advised of his rights, but it likely buys authorities no more than 48 hours.

During that time Tsarnaev, 19, will be questioned by a federal government team called the High Value Detainee Interrogation Group, consisting of officials of the FBI, CIA and Defense Department. Though he will not have a lawyer present, any statements he makes during the questioning will be admissible in court.

Among the questions investigators are certain to focus on is whether he and his brother  had help in plotting or carrying out the terrorist attack at the finish line of the marathon. The dual blasts from pressure cookers packed with explosives and shrapnel killed three people and injured 176.

That question took on more urgency when police in New Bedford, Mass., south of Boston, announced Friday evening that three people there had been taken into custody as part of the bombing investigation.

In addition to possible co-conspirators in the U.S., the interrogators also will want to know whether the brothers, both ethnic Chechens, received any assistance from overseas.

Travel records obtained by NBC New York showed that Tamerlan Tsarnaev left the country for six months in 2012, flying to Moscow on Jan. 12 and returning on July 17. Where he went and what he did after his arrival in Russia could expand what so far has been a domestic manhunt into a global one.

Enemy combatant?
Suspicions that the elder brother could have received terrorist training or support abroad were heightened Friday, when an official familiar with the matter told NBC News that a foreign government had expressed concern in 2011 that Tamerlan Tsarnaev could have ties to terrorism. The official said the FBI investigated, but found no such links and reported the findings back to the foreign government.

Even if authorities determine that the Tsarnaevs received support from an overseas terrorist organization, the Obama administration official said the government will not seek to declare him an enemy combatant and try him before a military commission, as it has done with senior al Qaeda officials captured overseas and imprisoned at the Guantanamo Bay detention camp. Administration officials see that scenario as a non-starter, the official said, particularly given the fact that Dzhokhar Tsarnaev is an American citizen, naturalized last September.

AP

Tamerlan Tsarnaev, left, was killed by police. Dzhokhar Tsarnaev was captured and will be interrogated by a special team of investigators.

Republican Sens. Lindsey Graham of South Carolina and John McCain of Arizona issued a statement late Friday urging that the administration hold Tsarnaev as an enemy combatant.

"It is absolutely vital the suspect be questioned for intelligence gathering purposes. We need to know about any possible future attacks which could take additional American lives," said the statement, posted on Graham's Facebook. "The least of our worries is a criminal trial which will likely be held years from now." 

Mass of evidence
At the same time they are seeking to uncover the bombing suspects’ motives and determine whether they had a support network, investigators will continue to collect and analyze vast amounts of forensic evidence from crime scenes stretching across three cities.

In addition to processing evidence from the bombings, FBI technicians will analyze hundreds of hours of video camera recordings from private and public surveillance and traffic cameras as they attempt to trace the brothers’ movements – both after the attack and before it.

Investigators also will obtain and assess phone records, seeing who the brothers were in contact with in the weeks and months leading up to the attacks.

Only when they have scrutinized every bit of data, and explored every lead, will they turn over the mountain of evidence they have assembled to prosecutors. It will be up to them to decide what charges the younger Tsarnaev should face and whether to seek the federal death penalty in a state where life in prison is the maximum sentence that can be imposed.

But despite such a massive expenditure of time and technological know-how, they may never answer the most haunting question surrounding the case, as President Barack Obama noted.

“Why,” he asked during a brief statement on Dzhokhar Tsarnaev’s arrest late Friday, “did young men who grew up and studied here as part of our communities and country resort to such violence?”

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