How civilian prosecution gave the U.S. a key informant

Navy Capt. John Murphy, the Pentagon’s chief war crimes prosecutor at the military commissions compound at Guantánamo Bay, Cuba, on Sunday May 31, 2009.
Navy Capt. John Murphy, the Pentagon’s chief war crimes prosecutor at the military commissions compound at Guantánamo Bay, Cuba, on Sunday May 31, 2009.

WASHINGTON One day in 2011, the top prosecutor in the system of military commissions set up after the Sept. 11 attacks to prosecute terrorists traveled to New York for a special meeting with Justice Department officials. A Somali terrorist, Ahmed Abdulkadir Warsame, was being held aboard a U.S. warship after being captured in international waters off Yemen, and the official, Navy Capt. John F. Murphy, wanted him tried at Guantánamo Bay before a military commission.

In an early test of President Barack Obama’s belief that international terrorists could be successfully prosecuted in the criminal courts, Murphy was overruled. Warsame was prosecuted in federal court in Manhattan, and after pleading guilty to providing material support to al-Shabab and al-Qaida in Yemen and to other charges, he became one of the nation’s most important terrorism informants.

To Justice Department and FBI officials, their success in prosecuting Warsame and eliciting important information from him was proof that an alternative legal system was not needed to keep the U.S. safe from terrorism. But that belief — a founding principle of Obama’s national security strategy – is about to be challenged by his successor, President Donald Trump.

Sen. Jeff Sessions, R-Alabama, Trump’s nominee for attorney general, has long believed that the Obama administration sacrificed valuable intelligence by bringing terrorism cases in federal court. Along with other Republicans in Congress, he has argued that the isolated military prison at Guantánamo is where such terrorists should be sent and tried.

Trump is expected to formally endorse that view with an executive order keeping Guantánamo open and then fill it with “bad dudes,” as he has put it.

But a look at Warsame’s case — and the substantial cooperation he provided to the military and law enforcement — suggests it could again become a flashpoint in a debate over which system — civilian or military — is best to handle terrorism cases.

Current and former law enforcement officials, some of whom spoke on the condition of anonymity because many details about Warsame’s capture and his value as a witness remain secret, agreed on his importance. Among informants in federal custody, the officials said, he ranks among a handful whose information seriously disrupted terrorist plots and contributed to winning convictions.

Warsame provided crucial intelligence about al-Shabab and al-Qaida leaders and helped thwart a terrorist attack in Saudi Arabia, the officials said. His assistance also helped in the hunt to find Anwar al-Awlaki, an American imam who became al-Qaida in Yemen’s chief propagandist; and it has underpinned terrorism prosecutions in federal courts in Manhattan, Brooklyn and Minnesota. With Warsame’s cooperation, the authorities also have secretly charged at least a dozen terrorists, including a top al-Shabab commander, who remain at large overseas.

Warsame’s cooperation was so significant that the military outlined it in a highly classified document that has never been made public.

“He ultimately proved to be one of the most important sources of intelligence,” said James McJunkin, the FBI’s former counterterrorism chief, who declined to discuss what Warsame provided to the government. “Many, including prominent Republicans in Congress, were claiming at the time that federal courts were not a place for terrorists. The facts prove exactly the opposite. These critics can’t point to anything that occurred in Gitmo other than a damn mess.”

By the time of Warsame’s arrest in 2011, al-Qaida in Yemen had, among other things, claimed credit for a Christmas Day 2009 attempt to blow up a Detroit-bound airliner and a 2010 plot to detonate bombs hidden in printer cartridges on flights heading for the U.S.

The possibility of the group’s collaborating with al-Shabab was a nightmare for U.S. officials, who were concerned that al-Qaida might arm al-Shabab to launch an attack on the West.

When U.S. intelligence discovered Warsame was in Yemen and preparing to travel to Somalia by boat from the Port of Aden, a mission was developed, code-named Operation Cypress, to capture him, officials said. A Navy SEAL team and an FBI agent with the Hostage Rescue Team parachuted into the region and waited for word that Warsame was on the boat.

The SEALs, disguised as Navy sailors conducting anti-piracy missions, boarded at least one vessel before finding a man who they believed was Warsame on April 19, 2011, and taking him back to a U.S. Navy ship, the Boxer. Warsame at first lied about his identity, but the FBI was able to verify it.

Warsame pleaded with his captors not to be sent to Guantánamo and started cooperating almost immediately.

His shipboard interrogation by the military, lasting more than two months, occurred without his being advised of his Miranda rights, since the questioning was for intelligence collection and not law enforcement purposes. During the interrogation, Warsame said that he had met with al-Awlaki and also Ibrahim Hassan al-Asiri, the chief bomb maker for al-Qaida in Yemen (who remains atop the military’s kill list.)

It was while this interrogation was taking place that Murphy, the chief military prosecutor, met with prosecutors in the U.S. attorney’s office in Manhattan. They were preparing a criminal case against Warsame.

In arguing that Warsame should be prosecuted at Guantánamo, Murphy noted the risks of a civilian trial, citing the acquittals in 2010 of Ahmed Khalfan Ghailani, an al-Qaida operative, of all but one of more than 280 charges stemming from the deadly 1998 bombings of two U.S. Embassies in East Africa. (Ghailani’s conviction on the remaining charge was nevertheless sufficient to earn him a life sentence.)

Murphy also noted that Warsame hadn’t been read his rights, raising the question of whether his statements would be admissible in federal court. He said that he could use them in a military commission.

The prosecutors disagreed. They suggested Warsame would continue talking after the military interrogation was over and after he was read his rights.

Bolstering their case against him were three cooperating witnesses in Minnesota who met Warsame in early 2008 at a safe house on the Somali coast where he was recuperating from a gunshot wound. Incriminating evidence was also found on Warsame when he was taken into custody: a laptop computer that he had been given by Samir Khan, an American member of al-Qaida in Yemen who worked on its online propaganda publication Inspire.

After further discussions at the highest levels of the Obama administration, the decision was made to pursue a federal prosecution of Warsame.

Aboard the Boxer, Warsame was given new guards and interrogators, including an FBI agent and former New York Police Department detective. The authorities changed the look of the room, displaying an FBI seal to clearly distinguish the purpose and circumstances of the new interrogation from the earlier one, and to ensure Warsame understood that his answers to the law enforcement questioning were voluntary.

After a break of several days, Warsame was read his rights, and he agreed to continue to talk. He was eventually taken to Djibouti, and from there, to New York in an FBI Gulfstream jet, arriving in early July 2011, when his capture was announced.

Al-Shabab and al-Qaida had no idea what had happened to him. And he continued to talk.

The dispute over where Warsame should be prosecuted occurred more than a year after the debate over where to try Khalid Sheik Mohammed, the admitted mastermind of the Sept. 11 attacks, and four other detainees accused in the attacks. The Obama administration ultimately dropped a plan to try them in federal court in Manhattan after strong opposition from local officials, deeply disappointing prosecutors who saw the cases as the best chance to hold the men responsible.

But it turned out that it has been hard to build a functioning judicial system from scratch, let alone a court that operates at a remote base far from where the judge and lawyers live.

Contributing to years of delays, defense lawyers have been able to mount repeated challenges to every procedural step because the rules of the tribunals system are untested, unlike those of civilian court.

The use of plea deals at Guantánamo is also largely untested, and because the government maintains that it can hold an al-Qaida prisoner indefinitely as a wartime detainee even after he serves a sentence or is acquitted, military prosecutors may not be able to assure someone who seeks to cooperate that he will be released after serving his sentence.

In contrast, the value of cooperation deals in federal terrorism prosecutions has been shown to be extremely effective.

Warsame helped prosecutors build a case against Khan, who later died in the drone strike that killed al-Awlaki. He also provided crucial information about a top al-Shabab commander known as “Ikrima,” who was later implicated in a 2013 attack on a mall in Nairobi, Kenya.

Warsame has yet to appear as a witness in a U.S. trial though in at least six cases in Minnesota, Brooklyn and Manhattan, the threat of his testimony appears to have helped persuade defendants to plead guilty.

In one case in which Warsame was expected to be a witness, the defendant, Mohamed Ibrahim Ahmed, pleaded guilty in 2012 to conspiracy charges and was sentenced to just over nine years.

“Those who had the misfortune to know Mr. Warsame,” Ahmed’s lawyer, Sabrina Shroff, said recently, “even in the most fleeting of moments, have spent years in American jails regretting that chance meeting.”

Eric Schmitt and Charlie Savage in Washington contributed reporting.