Terrorist Has Cooperated With U.S. Since Secret Guilty Plea in 2011, Papers Show

The terrorist, Ahmed Abdulkadir Warsame, served as a military commander with the Shabab in Somalia and worked as a liaison with Al Qaeda’s branch in Yemen, including brokering a deal for the Shabab to buy weapons directly from the Qaeda group, the government has said.

The newly unsealed court papers show Mr. Warsame pleaded guilty in a closed court proceeding in Manhattan in December 2011, about five months after he was brought to New York. After the plea, he met weekly with the government for hours at a time, disclosing intelligence information about his Shabab and Qaeda co-conspirators, who included “high-level international terrorist operatives,” prosecutors said in one highly redacted letter dated March 2012.

In the letter, the office of Preet Bharara, the United States attorney in Manhattan, asked a federal judge to keep Mr. Warsame’s plea confidential, noting that his information had opened new lines of investigation and developed new targets for the government.

Any publicity about his plea was quite likely to undermine the government’s ability to investigate and prosecute his associates and would also pose a threat to the safety of his family abroad, the office said.

Since it was announced in July 2011, the Warsame case has been seen as a test of the administration’s approach in the use of the military and civilian court systems and its desire not to send a new prisoner to the detention center in Guantánamo Bay, Cuba.

Mr. Warsame, a Somali in his mid-20s, commanded hundreds of fighters in battle in Somalia, and in 2009 and was sent by senior Shabab leaders to Yemen to train with the Qaeda group there, known as Al Qaeda in the Arabian Peninsula or AQAP, a prosecutor, Benjamin Naftalis, said in a 2011 document.

But the circumstances of his capture and interrogation prompted sharp debate. He was apprehended in April 2011 by the United States military in the Gulf of Aden, and questioned aboard a Navy ship for about two months by officials for intelligence purposes without being advised of his Miranda rights or given a lawyer.

After a four-day break, he was then advised of his rights, waived them and was questioned for about a week by law enforcement agents, the government has said. After that, he was brought to New York.

Mr. Bharara said Mr. Warsame’s capture, “his lengthy interrogation for intelligence purposes, followed by his thorough questioning by law enforcement agents, was an intelligence watershed.”

His handling represented “a seamless orchestration by our military, intelligence, and law enforcement agencies that significantly furthered our ability to find, fight and apprehend those who wish to do us harm,” Mr. Bharara added.

Lee Ginsberg, a lawyer for Mr. Warsame, declined to comment. Mr. Warsame pleaded guilty to nine counts. In court, he admitted to conspiring with others, including American citizens, to provide material support to the Shabab and Qaeda groups, and other charges.

The Americans are not identified, but Mr. Naftalis said in the 2011 document that several cooperating witnesses charged in Minnesota with traveling to Shabab training camps had interacted with Mr. Warsame in East Africa, and had corroborated information provided by him.

The New York Times also reported this month that Mr. Warsame had told the authorities about his encounters with Samir Khan, an American who worked with Al Qaeda in Yemen before he was killed in the same drone strike that killed the senior Qaeda operative Anwar al-Awlaki.

The documents also show that prosecutors had considered having Mr. Warsame testify in the trial of another defendant, Mohamed Ibrahim Ahmed, who eventually pleaded guilty last year to conspiring to support Al Shabab.

Sabrina Shroff, a lawyer for Mr. Ahmed, said it “boggles the mind” that prosecutors would have used Mr. Warsame against her client, adding, “It’s like you’re using the consigliere as a snitch against the soldier.”

The transcript of Mr. Warsame’s plea shows that he told Judge Colleen McMahon that he first “joined Al Shabab to fight the Ethiopian invasion of my native country, Somalia.”

Mr. Warsame faces a mandatory minimum sentence of life imprisonment, but Judge McMahon could impose far less time if he cooperates satisfactorily, the agreement shows.

It also says that at his request, prosecutors would also consider asking that Mr. Warsame and his family be placed in the witness protection program and relocated under a new identity.

His plea comes amid a series of new terrorism cases being sent for prosecution in the city’s federal courts, including that of Sulaiman Abu Ghaith, a son-in-law of Osama bin Laden who has pleaded not guilty to conspiracy to kill Americans.