By EDMUND MAHONY

                  SAN JUAN, Puerto Rico - When President Clinton in August offered clemency
                  to 16 radical Puerto Rican nationalists, he was freeing members of two groups
                  that were created in consultation with Cuban intelligence agents and that
                  bombed more than 120 U.S. targets with Cuban support since at least the
                  1970s.

                  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.''

                  Staff Writer Michael Remez contributed to this story.