Federal prosecutors in Chicago have indicted four alleged masterminds of the 2008 Mumbai attacks, including two men who have been linked by U.S. investigators and foreign court documents to Pakistan’s security forces.

The indictment filed Monday never mentions the Pakistani security forces or their alleged role in the attacks. But it represents a major development in a secretive and diplomatically sensitive prosecution set for trial next month, because Pakistan is considered a close U.S. ally in the fight against terrorism. Prosecutors charged the four Pakistanis with playing lead roles in the attacks, suspected to have been organized by the Lashkar-i-Taiba Islamist group, which killed 166 people, six of them Americans. Three of the four suspects are thought to be at large.

The indictment identifies a man known only as Major Iqbal as one of the masterminds, who allegedly directed and funded months of reconnaissance in Mumbai by David Coleman Headley, a mysterious Pakistani American businessman who was once an informant for the U.S. Drug Enforcement Administration. Headley was arrested in October 2009 and is cooperating with U.S. and Indian officials.

The indictment describes Iqbal as “a resident of Pakistan who participated in planning and funding attacks by Lashkar.” But as ProPublica has reported in The Washington Post, U.S. and Indian anti-terrorism officials and Indian court documents allege that Iqbal was a serving officer in Pakistan’s Inter-Services Intelligence agency. He allegedly acted as Headley’s main handler, one of at least three ISI officers suspected of involvement in recruiting, training and directing Headley in terrorist activities, according to U.S. and Indian investigators and Indian court documents.

The other significant figure indicted Monday is a longtime Lashkar chief named Sajid Mir, who also is accused of serving as Headley’s handler. Mir remains at large, according to investigators. He allegedly was a key plotter of the Mumbai attacks. His voice was caught on tape directing the slaughter by telephone from a safe house in Pakistan, according to officials and documents.

In 2007, French authorities convicted Mir of terrorism in absentia and accused him of being an officer of the Pakistani military and possibly the ISI. Some Western anti-terrorism officials think Mir spent time in the Pakistani security forces, while others say he was close to the ISI but was not a serving officer.

The other two suspects charged Monday are alleged Lashkar chiefs whose voices also were recorded directing the 10 gunmen who carried out the three-day siege in Mumbai. Suspect Abu Qahafa is accused of overseeing the training of the attack team. Suspect Mazhar Iqbal, alias Abu al-Qama, is the only one of the four known to be in custody. Pakistani authorities arrested him in early 2009 and charged him and six others in the Mumbai attacks, but that trial has apparently stalled.

All the four suspects were charged Monday with six counts of aiding and abetting the murder of U.S. citizens in India as well as providing material support to terrorists and conspiracy to murder. Mir, Qahafa and Iqbal were also charged with conspiracy to bomb public places in India, and Mir has been charged with directing a plot that involved Headley in Denmark. The four could face the death sentence or life in prison.

U.S. Justice Department spokesmen in Washington and Chicago declined to comment on the indictments.

A fifth defendant, who was charged earlier in the case, is in U.S. custody. Tahawwur Rana, a Chicago-based businessman, allegedly assisted Headley’s reconnaissance efforts in India and Denmark. Rana was arrested with Headley in 2009 and is set to go on trial in Chicago in May.

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