Jane Rosenberg

Courtroom sketch of Suleiman Abu Ghaith in New York federal court on Friday.

The arrest and trial of alleged al-Qaida spokesman Suleiman Abu Ghaith may resolve a long-standing debate inside the U.S. intelligence community on what Iranian officials did with members of the terrorist group who snuck into the country shortly after 9-11, hoping they would be treated, if not warmly, then as "the enemy of my enemy," as one U.S official put it.

Abu Ghaith, who was arraigned on Friday in federal court in New York on charges he plotted to kill Americans, described the conditions under which al-Qaida officials' were confined in Iran in a 22-page statement signed after his arrest last week in Jordan.

The statement, which was referenced in his court appearance, is expected to shed light on the accuracy of intelligence gathered by the U.S. in months after 9-11 indicating that the so-called al-Qaida “management council” detained in Iran was still conducting business, even discussing procurement of nuclear weapons.

The debate among U.S. intelligence officers and agencies centers on how Iran treated the al-Qaida leaders and bin Laden relatives following their capture in Iran in early 2002, and how much it they were allowed to communicate with other members of the terrorist group. The faction in Iran, which with family and bodyguards numbered in the hundreds, bribed their way into the country but was rounded up not long afterward. As one U.S. official told NBC News Thursday, what happened next occurred inside the "blackest of the black boxes" of Iran's intelligence apparatus.

Some analysts believe that members of the group were more or less placed under house arrest. Iranian officials denied that, saying they were "in jail."

Another question is whether the group had significant operational communications with other al-Qaida leaders. One high-ranking former U.S. official told NBC News this week that he was unaware of any contact regarding al-Qaida operations.

But George Tenet, director of the CIA following the 9-11 attacks, painted a different picture in his memoirs, "At the Center of the Storm," written with William Harlow.

In the book, Tenet described incidents in which he learned that the group was not only communicating with Saudi-based al-Qaida leaders on operational matters, but also trying to obtain nuclear weapons. 

"From the end of 2002 to the spring of 2003, we received a stream of reliable reporting that the senior al-Qaida leadership in Saudi Arabia was negotiating for the purchase of three Russian nuclear devices,” Tenet wrote. “Saudi al-Qaida chief Abu Bakr relayed the offer directly to the al-Qaida leadership in Iran, where Sayf al-Adl and (Mohammed) Abdel al-Aziz al-Masri (described as al-Qaida’s “nuclear chief” by Khalid Sheikh Mohammed) were reportedly being held under a loose form of house arrest by the Iranian regime.

Tenet wrote that the al-Qaida leaders had learned lessons from previous attempts to procure nuclear devices in the nuclear black market in the early 1990s.

“Saif al-Adel told Abu Bakr that no price was too high to pay if they could get their hands on such weapons,” he wrote. “However, he cautioned Abu Bakr that al-Qaida had been stung by scams in the past and that Pakistani specialists should be brought to Saudi Arabia to inspect the merchandise prior to purchase.

"As soon as I got wind of al-Qaida negotiations to purchase nuclear components in Saudi Arabia, I contacted the Saudi ambassador to the United States, Prince Bandar, and gave him all the details we had," Tenet said.

The CIA also communicated its intelligence to the Iranians, being uncertain of what the Islamic Republic knew of the communications, according to the former CIA director’s account.

"One senior al-Qaida operative told us that Mohammed Abdel al-Aziz al-Masri, who had been detained in Iran, managed al-Qaida’s nuclear program and had conducted experiments with explosives to test the effects of producing a nuclear yield. We passed this information to the Iranians in the hope that they would recognize our common interest in preventing any attack against U.S. interests."

Another U.S. security official told NBC News that Tenet's message did get attention in Tehran and that, in 2003, the group in Iran’s communications with other al-Qaida leaders were down.

Beyond the historical debate, U.S. officials want to know what happened to the other leaders in the management council. Apart from Khalid Sheikh Mohammed, who is awaiting trial before a U.S. military court, the whereabouts of the others are unknown. There have been  intermittent reports over the years that Saif al-Adel, the Egyptian-born military director of al-Qaida, was permitted to leave Iran, but they have not been confirmed.  

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Osama bin Laden's son-in-law, who acted as a spokesman for al-Qaida, has been apprehended, transported to New York and charged with conspiracy to kill Americans, according to court documents unsealed Thursday.

Sulaiman Abu Ghaith appeared alongside bin Laden in a 2001 video in which they took responsibility for the 9/11 attacks and warned of more, before he dropped out of sight for more than a decade before his arrest.

"I commend our CIA and FBI, our allies in Jordan, and President Obama for their capture of al-Qaida spokesman Sulaiman Abu Ghaith," said Rep. Peter King, R-N.Y., a member of the Homeland Security Committee, who first announced the news. 

"I trust he received a vigorous interrogation, and will face swift and certain justice," added King, who is also chairman of the Sub-Committee on Counterterrorism and Intelligence.

Prosecutors say from at least May 2001 to around 2002, Abu Ghaith served alongside bin Laden, appearing with him and his then-deputy Ayman al-Zawahiri, speaking on behalf of the terrorist organization and in support of its mission, and warning that attacks similar to those of September 11, 2001 would continue.

The government says around May 2001, Abu Ghaith urged individuals at a guest house in Kandahar, Afghanistan, to swear allegiance to bin Laden. On the evening of Sept. 11, 2001, after the terrorist attacks on the United States, bin Laden summoned Abu Ghaith and asked for his assistance. He agreed to provide it.

On the morning of Sept. 12, 2001, Abu Ghaith appeared with bin Laden and Zawahiri, and spoke on behalf of al-Qaida, warning the United States and its allies that "[a] great army is gathering against you" and called upon "the nation of Islam" to do battle against "the Jews, the Christians and the Americans," the court document says.

Also, after the September 11, 2001 terrorist attacks, Abu Ghaith delivered a speech in which he addressed the then-U.S. Secretary of State and warned that "the storms shall not stop, especially the Airplanes Storm," and advised Muslims, children, and opponents of the United States "not to board any aircraft and not to live in high rises."

Abu Ghaith arranged to be, and was, successfully smuggled from Afghanistan into Iran in 2002, where he spent most of the decade, U.S. officials said.

Even as government officials applauded the arrest of Abu Ghaith, his transport to the United States stirred controversy among lawmakers who were apparently caught by surprise by the news.

"We believe the administration's decision here to bring this person to New York City, if that's what's happened, without letting Congress know is a very bad precedent to set," said Sen. Lindsey Graham, R-S.C., who held a press conference with Sen. Kelly Ayotte, R-N.H.

"And when we find somebody like this, this close to bin Laden and the senior al-Qaida leadership, the last thing in the world we want to do, in my opinion, is put them in civilian court. This man should be in Guantanamo Bay," Ayotte said.

"So we're putting the administration on notice," said Graham. "We think that sneaking this guy into the country, clearly going around the intent of Congress when it comes to enemy combatants, will be challenged."

Earlier, in an interview on MSNBC, House Intelligence Chair Mike Rogers, R-Mich., strongly criticized the administration for bringing Abu Ghaith to the United States.

Rogers, a former FBI agent, said that Mirandizing a top al-Qaida suspect and bringing him to the United States for trial creates a host of problems — instead of sending him to the facility at Guantanamo Bay, Cuba, which was built to handle high value prisoners.

"Al-Qaida leaders captured on the battlefield should not be brought to the United States to stand trial," Rogers said. "We should treat enemy combatants like the enemy. The U.S. court system is not the appropriate venue."

The Obama administration has been trying to clear out Guantanamo and not bring any new prisoners there.

Sen. Charles Schumer, D-N.Y., said it's fine with him if Abu Ghaith is put on trial in New York because key state and city officials had been consulted in advance, unlike in the case of terror suspect Khalid Sheikh Mohammed.

"Unlike with KSM, Kelly and others had been consulted ahead of time about this and they gave the green light to do it. As you know, (Police Commissioner) Ray Kelly, Mayor (Michael) Bloomberg and I opposed the trial of (Mohammed) in New York and we successfully made sure that didn't happen," said Schumer. "On issues like this, I defer to Commissioner Kelly, and I think the mayor does as well. And he thinks it's OK to do it here, and I'll go by that," Schumer said. 

Rapho-Gamma via Getty Images

Al-Qaida spokesman Sulaiman Abu Ghaith, left, and Osama bin Laden in a photo taken from a video and released by Al Jazeera in 2001. In the video, which emerged shortly after the 9/11 attacks, Abu Gaith said: "Americans should know the storm of planes will not stop."

Jordanian sources confirmed that Abu Ghaith was sent by Turkey via Jordan to Kuwait, and intercepted in Jordan and brought to the U.S.

According to the officials, who spoke on condition of anonymity, Turkish officials captured Abu Ghaith in the capital Ankara, where a court ruled he had entered the country illegally with a fake passport. The Turkish government then ostensibly deported Abu Ghaith to his birthplace Kuwait, but arranged for him to transit through Jordan where he was ultimately taken into custody by U.S. law enforcement, the officials said.

U.S. officials told NBC that prior to his interception in Turkey, Abu Ghaith, who dropped out of sight after 2002, had spent most of a decade in Iran.

"Nobody's heard a peep. Some people thought he was being held prisoner in Iran, others thought he might be dead," said Evan Kohlmann, an American counter-terrorism analyst for NBC News. 

NBC News chief Pentagon correspondent Jim Miklaszewski and Moufaq Khatib NBC News producer in Jordan contributed to this report.

This story was originally published on Thu Mar 7, 2013 11:47 AM EST