Mr. Headley himself is not on trial. But he will be the main witness against Tahawwur Hussain Rana, a Chicago businessman who is accused of providing financial and logistical support for the 2008 siege in Mumbai. The attack, a barrage of gunfire and grenades, killed at least 163 people, including six Americans. Mr. Rana’s defense is that he agreed to support Mr. Headley’s activities in India because he was led to believe he was working for the ISI, and therefore the Pakistani government.

Bruce O. Riedel, a terrorism expert at the Brookings Institution and former Central Intelligence Agency officer, predicted that the trial would be “the next nail in the coffin of U.S.-Pakistan relations, as the ISI’s role in the murder of six Americans is revealed in graphic detail.”

American authorities have kept much of the evidence secret. Citing national security concerns, they have successfully moved to quash the defense lawyers’ subpoenas for State Department cables and records held by the F.B.I. that discuss Pakistan’s links with militants.

And though the government has charged four other men, including the officer known as Major Iqbal, with aiding and abetting the murder of American citizens, the indictment refers to them either as commanders or associates of the militant group Lashkar-e-Taiba, not as having links to the ISI.

In interviews in recent days, American military and intelligence officials who have served in Pakistan argued that the ISI’s story is complex. Some of them portray it as an unwieldy bureaucracy that even Pakistani generals struggle to control. The United States should try to reform the ISI, they argue, not abandon it.

“I think we’re at an extremely critical juncture,” said James Helmly, a retired general who served as the senior American military representative in Pakistan from 2006-8. “We need to mature the relationship.”

Arguably the most feared institution in Pakistan, the ISI has a mythic reputation among Pakistanis as a shadow government with a hand in virtually every major development in the country. Human rights and democracy activists say the agency is out of control and accuse it of carrying out hundreds of disappearances, systematically rigging elections and harassing civilians who support peace with India.