The Mystery of What Happened to a 9/11 Suspect’s Sons

The fate of the sons of Khalid Shaikh Mohammed, the man accused of being the mastermind of the Sept. 11, 2001, attacks, has long been a source of mystery and controversy.

Two of the boys were 8 and 10 when they were captured by Pakistani authorities in 2002.

A psychologist who waterboarded Mr. Mohammed during interrogations in Poland has admitted that he threatened to slit the throat of one of the boys. During another interrogation, the prisoner has said, he thought he heard his children crying in the next room.

But a prosecutor has now disclosed that the boys were never in U.S. custody. Nor were two younger boys, believed to be 5 and 6, who were present during a joint U.S.-Pakistani raid that captured Mr. Mohammed in 2003.

Nonetheless, “the children would be an ever-present emotional bargaining chip in the interrogation and torture sessions that followed,” Mr. Mohammed’s military lawyer, Lt. William Xu, told the judge in pretrial hearings at Guantánamo Bay, Cuba.

Mr. Mohammed’s lawyers have been seeking a court order for more information about what happened to the boys. They argue it could bolster an effort to have the case dismissed for “outrageous government conduct” because that was part of his torture. If Mr. Mohammed is convicted, they have said they might want to present the story of what happened to the boys to a military jury to argue that he should be spared capital punishment.

An earlier judge rejected the effort as a “fruitless scavenger hunt,” according to Capt. Tara J. Arndt, a case prosecutor.

But testimony has shown that C.I.A. agents used threats to the boys as an interrogation tool before he was transferred to Guantánamo in 2006. The case has yet to reach the trial phase as defense lawyers seek to suppress some evidence that they say was derived from torture and surface other information in their efforts to defend him.

James E. Mitchell, the contract psychologist who worked for the C.I.A., testified in 2020 that he had consulted a lawyer for the agency and obtained permission to threaten to kill one of Mr. Mohammed’s sons. During that month, Mr. Mitchell waterboarded Mr. Mohammed 183 times.

The lawyer said the threat would not constitute torture if they were conditional and did not suggest that the boys faced “imminent harm,” Mr. Mitchell testified. So he told Mr. Mohammed that, if another child died in a terrorism attack in the United States, “then I will cut your son’s throat.”

Looking back, it was “distasteful,” Dr. Mitchell testified. He added that eight children died in the Sept. 11 attacks, which Mr. Mohammed is accused of orchestrating and killed about 3,000 people.

In court last week, Frank Pellegrino, a retired F.B.I. agent who obtained a confession from Mr. Mohammed in 2007, said the threat was “a horrible thing to say.” He later called the C.I.A. program that imprisoned Mr. Mohammed a “flaming bag of crap.”

But he testified that Mr. Mohammed had voluntarily confessed to his role in the Sept. 11 plot during an interrogation at Guantánamo nearly four years later.

The prisoner’s children figured in that interrogation too. On the fourth and final day of their meetings, Mr. Pellegrino said, Mr. Mohammed asked for some family photos that U.S. authorities had taken from him before the interrogation. Mr. Pellegrino said he arranged for them to be returned.

Prosecutors provided the defense with everything they deemed relevant, plus material that “exceeded the scope of the government’s obligations,” Captain Arndt said.

The boys who were captured in 2002 “were never in United States custody and there are no known statements of those children,” she told Col. Matthew N. McCall, the fourth judge to preside in the long-running case. She said the prosecution also determined that the younger two boys “were never taken into custody at all. There are no records indicating that the children were mistreated in any way.”

Mr. Mohammed would not know what became of the younger children until after he reached Guantánamo in 2006 and met with representatives of the International Committee of the Red Cross. By then, they were believed to be living with their mother in Iran, where she moved with her eight children after her husband was captured.

In early 2007, Mr. Mohammed said in conversations with the U.S. military and F.B.I. that the older boys had been held for four or five months. In one account, he described them “as bait” to get him to turn himself in, which he did not do. They were then dropped off at a mosque with a religious school.

Mr. Mohammed told the F.B.I. agents that his younger sons had been taken into custody at the time of his 2003 arrest.

“From the very beginning, these young children were used against Mr. Mohammad during questioning,” Lieutenant Xu said. “He recalls being in the interrogation room and hearing his children crying in the next room and having the interrogator tell him that you, you can stop what you’re hearing.”

Apparently he was told at one point in his C.I.A. detention that the boys had been released. Then after a seven-hour torture session, he was told that his sons “had been detained again,” according to a C.I.A. report cited by Lieutenant Xu.

C.I.A. guards then shackled Mr. Mohammed in a standing position to deprive him of sleep, the report said, while he struggled “to control his emotions … possibly with concern over his sons.”