The Doctor and Joe visit the Master (Roger Delgado), imprisoned on a small island in the English Channel. He says he’s reformed but refuses to give up the location of his TARDIS. Hearing stories of ships vanishing mysteriously, the Doctor and Joe investigate a sea-fortress, where they are attacked by water-breathing bipedal Reptilians referred to as Sea-Devils. They escape and seek help at a nearby naval base.
The Doctor discovers that the Master, aided by his jailer Colonel Trenchard (Clive Morton), is stealing electrical equipment from the naval base to build a machine that will control the Sea-Devils to use them—you guessed it!—to build an army with which to conquer the world. The creatures begin to rise out of the sea in response to the Master’s summons. Trenchard is killed during the battle for the prison. The Doctor and Joe flee to the naval base again, where Captain Hart (Edwin Richfield) reports the disappearance of a submarine. The Doctor is seized by the sea creatures.
The Doctor offers to negotiate peace between the creatures and the humans, as he had tried to do with the Silurians. Robert Walker (Martin Boddey) a British politician, intends to do the same thing to the Sea-Devils that UNIT had done to the Silurians—bomb them. They begin using depth charges and intend to escalate to nuclear weapons. At the naval base, the Doctor persuades Walker to allow him one more chance at peace. In the meantime, urged on by the Master, the Sea-Devils capture the base.
The Master forces him to build a machine that will revive sleeping Sea-Devils all over the world. Once this is activated, the Sea-Devils turn on both Time-Lords, imprisoning them together. But the Doctor has sabotaged the machine. Using equipment from the captured submarine, they escape. The sabotaged machine destroys the Sea-Devil base before the Military can nuke it. The Master manages—of course—to escape.
Written by Malcolm Hulke, the story was filmed on HM Naval Base Portsmouth, No Man’s Land Fort, The Isle of Wight, and HMS Reclaim. The Royal Navy was happy to co-operate, waiving royalty fees and allowing sailors to volunteer as extras. The model of a submarine was created out of a submarine model kit from Woolworths, but the propeller was altered. Unfortunately, it now resembled an actual prototype being developed by the Ministry of Defense. The Director received a visit from two Naval Intelligence Officers, asking where they had gotten the idea. Doctor Who and the Silurians had received so many letters from scientists complaining that reptilians could not have lived in the Silurian Era that dialog was added to this story in which the Doctor admits that the name Silurian is inaccurate and the creatures should have been called Eocenes. The music used was electronic and synthesised—sea-creature weird, but not very likeable. This was the story in which Jon Pertwee first used the line, “reverse the polarity of the neutron flow,” which later became a running joke.