It may be years, if ever, before the world learns whether Pakistan’s powerful Inter-Services Intelligence Directorate (ISI) helped hide Osama bin Laden.

But detailed allegations of ISI involvement in terrorism will soon be made public in a federal courtroom in Chicago, where prosecutors last week quietly charged a suspected ISI major with helping to plot the murders of six Americans in the 2008 Mumbai attacks.

The indictment has explosive implications because Washington and Islamabad are struggling to preserve their fragile relationship. The ISI has long been suspected of secretly aiding terrorist groups while serving as a U.S. ally in the fight against terror. The discovery that bin Laden spent years in a fortress-like compound surrounded by military facilities in Abbottabad has heightened those suspicions and reinforced the accusations that the ISI was involved in the Mumbai attacks that killed 166 people.

“It’s very, very troubling,” said Congressman Frank Wolf, R-Va., chairman of the House Appropriations sub-committee that oversees funding of the Justice Department. Wolf has closely followed the Mumbai case and wants an independent study group to review South Asia policy top-to-bottom.

“Keep in mind that we’ve given billions of dollars to the Pakistani government,” he said. “In light of what’s taken place with bin Laden, the whole issue raises serious problems and questions.”

Three chiefs of Lashkar-i-Taiba, the Pakistani terrorist group, were also indicted in Chicago. They include Sajid Mir, a suspected Mumbai mastermind whose voice was caught on tape directing the three-day slaughter by phone from Pakistan. Mir, too, has links to the ISI. He remains at large along with the suspected ISI major and half-a-dozen other top suspects.

Despite the unprecedented terrorism charges implicating a Pakistani officer, the Justice Department and other agencies did not issue press releases, hold a news conference or make any comments when the indictment was issued last week. The 33-page document names the suspect only as “Major Iqbal.” It does not mention the ISI, although Iqbal’s affiliation to the spy agency has been detailed in U.S. and Indian case files and by anti-terror officials in interviews with ProPublica over the past year.

“Obviously there has been a push to be low-key,” said an Obama Administration official who spoke in an interview last week and requested anonymity because of the pending trial. “There is a desire to make sure the handling of the case doesn’t mess up the relationship” with Pakistan.

The first public airing of the ISI’s alleged involvement in the Mumbai attack will begin on May 16 with the trial of Tahawwur Rana, owner of a Chicago immigration consulting firm. Rana was arrested in 2009 and charged with material support of terrorism in the same case in which the four suspects were indicted last week. The star witness will be David Coleman Headley, a Pakistani-American businessman-turned-militant who has pleaded guilty to scouting targets in India and Denmark. Rana allegedly helped Headley use his firm as a cover for reconnaissance.

Rana’s attorney, Charles Swift, contends that Rana is not a terrorist because he thought he was assisting the ISI with an espionage operation. Swift said the U.S. indictment omits the ISI in hopes of mitigating tensions.

“The U.S. is attempting to walk a fine line between disclosure and non-disclosure,” Swift said. “What’s unusual is that the reason is to protect diplomatic relations... This indictment answers a few questions, but like everything else in this case, it raises even more.”

Even before the bin Laden slaying, the Obama Administration had taken a tougher tone about the ISI’s alleged links to militants. But a U.S. official said this week that U.S. counter-terror agencies still think that any involvement in the Mumbai attacks was limited to rogue officers.

“No one is saying we can’t work with the ISI—people are just pointing out the problems that exist,” said the official, who requested anonymity because of the sensitivity of the issue. “I think the problems are largely with individual officers as opposed to the institution.”

Pakistani officials deny that the security forces were involved in Mumbai. A senior Pakistani official questioned the credibility of Headley, who was an informant for the Drug Enforcement Administration when he began training with Lashkar in 2002.

“When somebody is a double agent, whatever he says in a U.S. court is not credible from our perspective,” said the official, who requested anonymity because of the pending trial. “There is no Major Iqbal serving in the ISI who has been involved in the Mumbai attacks.”

Headley has opened a door into an underworld in which spies, soldiers and terrorists converge. Although most of the prosecution's documents in the voluminous Chicago court file remain sealed, a recent judge’s ruling in the Rana case says Headley admitted to working for the ISI as well as for Lashkar and al Qaeda.

“I also told [Rana] about my meetings with Major Iqbal, and told him how I had been asked to perform espionage work for ISI,” Headley testified, according to the April 1 document. “I told [Defendant] about my assignment to conduct surveillance in Mumbai…I told him that Major Iqbal would be providing money to pay for the expenses.”

Headley described an almost symbiotic bond between Lashkar and the ISI, which helped create the group as a proxy army against India. His account has been corroborated through other testimony, communications intercepts, the contents of his computer and records of phone and e-mail contact with ISI officers, anti-terror officials say.

Senior ISI officers served as handlers for Lashkar chiefs and provided a boat, funds and technical expertise for the Mumbai strike, according to a 119-page report by India’s National Investigation Agency on its interrogation of Headley last year in Chicago.

Headley trained in Lashkar camps before being recruited in 2006 by an ISI officer, Major Samir Ali, who referred him to Iqbal in Lahore, the report says. Iqbal became Headley’s handler, introducing him to a Lt. Col. Shah and giving him months of spy training before deploying him to India, according to the Indian report, which officials say repeats Headley’s confessions to the FBI.

The U.S. indictment alleges that Iqbal gave the American $28,000 for the front company in Mumbai and other expenses. Iqbal and Mir directed Headley’s scouting of luxury hotels and other targets chosen to ensure that Americans and other Westerners would die. The two handlers met separately with Headley to discuss missions and receive his videos and reports, the indictment says. Iqbal took part in the decision to hit a Jewish center run by an American rabbi, who was killed along with his pregnant wife, according to the Indian report and U.S. investigators.

Headley also met at least twice with Iqbal in late 2008 to launch a Lashkar plot against a Danish newspaper that had printed cartoons of the Prophet Mohamed, according to the Indian report and investigators. Prosecutors charged Mir in the Denmark case but did not mention the suspected role of the major, who ended contact with Headley in early 2009 when Lashkar put the plot on hold, according to court documents.

But Headley stayed in touch with the other two ISI officers as he continued the Denmark plot for al Qaeda, according to investigators. His al Qaeda interlocutor was allegedly a well-connected former Pakistani Army major, Abdur-Rehman Syed, whose ISI handler was Col Shah and who had contacts with bin Laden, the report says.

“Rehman is directly in touch with the top...of al Qaida including Ilyas Kashmiri who is now the number 3 in the al Qaida hierarchy in Pakistan,” the report says. “Rehman has met Osama a number of times. [Rehman] once told Headley that his set up has been given the name...Army of Fidayeens by Osama bin Laden himself.”

Sajjan Gohel of the Asia-Pacific Foundation, a London security consulting firm, pointed to another possible link between the Mumbai case and bin Laden. The spy agency’s director during the period that the Mumbai plot developed was Gen. Nadeem Taj. Two months before Lashkar struck Mumbai in November 2008, Taj stepped down, reportedly as the result of U.S. pressure.

Before taking leadership of the ISI, Taj was commandant of the military academy in Abbottabad, the city where bin Laden was found on Sunday. Taj has been sued in federal court in New York by families of the victims of Mumbai for his alleged role in their deaths.

Gohel said the United States and Pakistan are “moving from ‘frenemies’ to outright enemies.”

“If the ISI were involved in protecting bin Laden, that means they were capable of protecting any terrorist in Pakistan,” he said. “It also means US citizens were acceptable targets. It illustrates the fact that since 9/11 the ISI has been duplicitous, disingenuous and potentially allowed acts of terrorism to be exported from its territory.”

Despite the increasing tensions with Pakistan, the U.S. official credited the ISI with helping in the hunt for bin Laden.

“There are lots of pieces of evidence that got us to where we are today,” the official said. “Some of those pieces were facilitated by the ISI. We have to look at the full scope of our relationship.”

That relationship can survive, the Pakistani official said.

“Both countries are allies, and important allies,” he said. “I think our relationship is beyond Headley’s statements in court.”