The Seaview is on a joint mission with Russian scientists to salvage the remains of a Soviet undersea lab. While a scientist is being lowered in the diving bell, a giant whale arrives and rams the bell. The glass is shattered, killing him.

Nelson and the remaining Russian scientist, Katya Markova, go on a second dive. The whale reappears, this time swallowing the diving bell whole! Now it's a race against thime as Captain Crane and the crew of the Seaview find the diving bell and get it out before Nelson and Markova run out of oxygen!

A missile defense platform-drone malfunctions and threatens to destroy the East Coast of the US.

Dr. Alex Holden is hunting a gigantic whale in which he has injected an experimental growth serum. It turns and destroys his boat, killing his crew. He is rescued by Seaview, which was on en route to plant a nuclear device to blast an undersea channel Holden obsesses over getting his swallowed equipment from the whale when it turns and comes at the sub, swallowing the bomb as it is being lowered! Nelson cannot detonate the bomb, as the president's carrier is in the area. The nearly insane Holden steals Nelson's remote detonating device and threatens to blow up the whale if he's not permitted to get samples of the whale.

Faceless aliens invade Earth and try to take over an underwater atomic base. The leader takes the form of an old, deseased friend of Admiral Nelson in order to convice Nelson they mean no harm. Nelson will have none of it and leads a landing party to the base to stop the aliens, even if the cost includes their own lives.