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.