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The three book series takes place on a submersible aircraft carrier which starts to have strange encounters with unknown creatures swimming in the ocean. As they continue to investigate, they encounter flying saucer UFOs, 50-year-old conspiracies and secrets involving previous encounters, and they capture and learn to operate the alien craft.

The sub-carrier has both an aircraft wing and a marine company onboard and eventually gains a group from a secret government group studying and working against the aliens.

I think there were several groups of bad aliens, some just worker animal like and the others really bad and a group of good aliens trying to keep worlds not ready from being preyed upon.

These books were written in the late eighties or early nineties, not totally sure.

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Is it the Starsea Invaders series by G. Harry Stine?

The Pacific Island port of Makasar used to be a fairly peaceful outpost of the United States Navy. But now, entire American families are vanishing without a trace and no one has any ideas about where they might be. William M. Corry, captain of the super-sub U.S.S. Shenandoah has orders to get to the bottom of the mysterious disappearances. At first, he suspects the unpredictable Chinese troopers patrolling the area, but after a little investigating, Corry realizes that the disappearances of the Americans cannot be the fault of the Chinese--they are as worried as he is. Corry refuses to believe the wild rumors of native cannibals until he accidentally unearths the real enemy: a force with power beyond anything humankind has ever known!

This is a guess because I haven't read the books and I cannot find a copy to check. But the description sounds similar to yours. The description of the second book mentions:

William M. Corry, captain of the American super-sub, the U.S.S. Shenandoah, was certain his new mission was not as simple as it first seemed. His initial orders were for a shakedown cruise, but those were quickly countermanded by another directive to proceed to the Solomon Islands. Yet Corry's gut feeling was that this was all a coverup for something far bigger. And he was about to be proved right! Told to rendezvous with and take on board a scientific team, Corry learned that the Shenandoah was at last going to be allowed to track down the alien invaders who were based beneath the sea--and this time they were going to bring one of the creatures back alive!

It is a trilogy and the publication date matches as the three books were written in 1993, 1994 and 1995.

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