The link between Cuba and the Puerto Rican independence movement is rarely mentioned in news accounts of bombings and other violent acts, even though it has been an accepted fact among some counterterrorism experts since the early 1960s. When a U.S. Senate subcommittee warned of the connection in 1975, its report also went largely unnoticed.

A two-year FBI investigation of the 1983 Wells Fargo robbery in West Hartford documented in striking detail how Cuban support for the Puerto Rican independence movement played out on a day-to-day basis during the most violent period of the movement's modern history. But the results of that investigation, as it touched on the Cubans, were not disclosed - until now.

Employing eavesdropping equipment and exhaustive surveillance, the FBI collected what at times amounted to running accounts of conversations and meetings between Cuban intelligence agents and members of the pro-independence group Los Macheteros.

Based on the evidence, the bureau concluded in a confidential briefing memo that: ''Numerous court-authorized interceptions of conversations between the Macheteros leaders have determined that the Cubans support and direct the Macheteros at a firsthand level.''

In addition to analyzing the FBI investigation, The Courant spent six months revisiting the scene of meetings between the Puerto Rican independentistas and their Cuban contacts, interviewing 50 sources including former Cuban agents, FBI agents and investigators for the U.S. Congress; and reviewing hundreds of pages of documents. The newspaper's examination reveals that the violent nationalist movement - at least from the early 1960s to the mid-1980s - was an essentially unified movement supported by senior Cuban officials.

Clinton offered clemency to some members of the closely allied FALN, the Spanish acronym for the Armed Forces of National Liberation, and Los Macheteros - ''The Machete Wielders.''

The FALN claimed credit for bombing scores of targets on the mainland United States; its 1975 bombing of Fraunces Tavern in New York killed four and injured 63. Los Macheteros, with the exception of the $7.1 million Wells Fargo robbery in West Hartford in 1983, limited itself to a separate front, bombing and assassinating targets in Puerto Rico.

In its Wells Fargo investigation, the FBI learned that Machetero leaders met most regularly with their Cuban contacts in Mexico City. But there was also less frequent travel to Cuba by the group's leadership. The meetings that took place outside the United States were monitored by the CIA.

The FBI determined that the Macheteros were meeting principally with four senior officers of the Cuban diplomatic-intelligence establishment. The Cuban agency most involved with Puerto Rican terrorism was the Department of the Americas, the agency responsible for Cuban intelligence operations in the Western Hemisphere.

When the FBI closed its Wells Fargo investigation in 1985, a group within the bureau argued - unsuccessfully, it turned out - that the U.S. Department of Justice list the four Cuban officers as unindicted co-conspirators in the Wells Fargo indictment.

A now-retired FBI counterterrorism officer said he never learned why the Cubans were left out of the indictment. A Cuban source speculated that the U.S. Department of State did not want to jeopardize indirect talks between the two countries that could have affected Cuban activity in Africa.

''I don't think it was in Cuba's interest to assist in an armed robbery in the United States in 1983,'' the retired FBI officer said recently. ''But the fact is, it did happen. And we documented it on tape. The thing that always amazed me was that it didn't cause a ripple. I was absolutely amazed.

''They were talking about Fidel. This was being decided at the highest levels in Cuba. This wasn't something the Cubans were spending a lot of time on. But the head of the Department of the Americas was involved.

''Nobody was particulary interested in listing these people as co-conspirators, which I thought was almost criminal. Because I thought we had an opportunity which went beyond sort of addressing a chronic thorn in the foot of Puerto Rico. But for reasons that I am yet at a loss to understand, that never happened.''

Several FBI and Justice Department officials who were involved in the Wells Fargo case said they have never understood why the extensive evidence of Cuban support for radical Puerto Rican nationalism received only scant attention among policy makers and in the press.

The White House, asked whether Cuban support for the Puerto Rican nationalists was considered during deliberations leading to the clemency offer, repeated an earlier assertion that decisions about clemency are confidential. Spokesman Jim Kennedy said advisers could be reluctant to express opinions if they were to become public.

''The details of what the president was advised, what facts were or were not brought to his attention, have not been disclosed,'' Kennedy said. The president ''made his decision after a careful and balanced consideration of the facts, the law and the differing points of view on the subject. The president has not changed his view of this matter.''

The Puerto Rican nationalists have consistently dimissed suggestions of Cuban support for their movement - even when presented with evidence that Cuba received about a third of the stolen Wells Fargo money.

Filiberto Ojeda Rios, partriarch of the violent wing of the independence movement, became agitated 18 months ago during a clandestine interview touching on the subject with Puerto Rican radio journalist Luis Penchi. Ojeda was asked, among other things, whether Cuba was given the stolen money.

''That is ridiculous,'' Ojeda said. ''Not only did that money not remain in Cuba; that money never went to Cuba. Whoever says that wants to give a bad name to. . . . That is ridiculous, absurd. I don't know where that version came from, nor am I going to ask you, but I am going to tell you that it is completely false, ridiculous and there is nothing to discuss.''

A spokesman for the Cuban Interests Section, which serves as Havana's de facto embassy in Washington, dismissed suggestions that Cuba supported the violent nationalists. ''I have no information on that,'' said Luis M. Fernandez. ''In my opinion, it is more science fiction than anything else.''