Poor Captain Crane. The things he had to go through. This time, he's in the Flying Sub, when he receives a distress call from the Seaview. He comes back to his sub, only to find it abandoned -- again. But wait, there's a force-field on the spiral stairs which knocks Crane out, and there's a stranger aboard who naturally shoots at him. Eventually Crane sees the crew, and he hears the voice of Nelson calling him a traitor. It takes about an hour, and a bullet in the shoulder (fired by guess who?), before Crane discovers aliens are testing the human race.

Naval ships have been disappearing, and Seaview is on a hunt for the undersea installation responsible. They find a sea-lab that is not only well-armed but surrounded by overgrown and ferocious sea-creatures. To complicate matters, the guest expert aboard is a traitor. Various "dangerous denizens" of the deep from earlier episodes reappear here, thanks to re-used footage: there's a whale, and one of those globular-eyed bottom-dwelling monsters seen in such episodes as "Deadly Creature Below".

"... but the Flying Sub's my baby!" Captain Crane to Chief Sharkey Seaview's reactor is running wild -- again. Without taking the time to don protective anti-radiation gear, Captain Crane runs into the Reactor Room to shut down the pile. An explosion renders him unconscious. Although treated in Sickbay with a special anti-radiation device, the Captain does not come out of his coma-like state. Doc can find no explanation. (Apparently, Doc hasn't read the script.) Corpsman Mallory has turned that life-saving device into a time-machine. Mallory is testing his fourth-dimension gadget on Crane before using it to enslave the entire world! A warped and insane Captain Crane from the future shoots and kills Admiral Nelson, because he believes the Admiral has held him back from achieving all he should have. Maybe he's paying Nelson back for the Krueger incident.