The seaQuest discovers the lost Library of Alexandria sunken beneath the sea.

However, when surrounding nations cannot agree on a peaceful way to share the discovery, Bridger must act as mediator before escalating tensions result in the destruction of the library.

Commander Ford, Dr. Westphalen, Lucas and Lieutenant Krieg are trapped on the surface of the ocean as a hurricane rages above them.

Meanwhile, suffering severe damage from a lightning strike, the seaQuest must desperately search for a sunken French submarine before its passengers, all children, run out of air.

The first manned mission to Mars returns home to Earth, led by Commander Scott Keller, an old friend of Bridger's.

However, a malfunction during re-entry plunges the capsule into the ocean where a corrupt general from a foreign confederation races to recover the astronauts before the seaQuest can.

In preparation for an experiment, the crew evacuates the seaQuest, leaving only Commander Ford, Lt. Commander Hitchcock, Lieutenant Krieg, Chief Crocker, and Lucas aboard.

However, environmental extremists use the seaQuest's vulnerable state to seize control of the boat.

The seaQuest makes the biggest discovery in Human history when they discover an alien starship entombed in an undersea rock face; trapped there for over a million years.

When an away team goes inside the ship, they find that they might not be the only thing aboard it.