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.