The Doctor and Jo are visiting the Master (Roger Delgado), who is being held prisoner in a converted castle situated on an offshore island. He seems fit and well and apparently resigned to life under lock and key. When the Doctor and Jo leave, Colonel Trenchard (Clive Morton), the governor of the prison, is revealed to be working with the Master to some unknown end. 

Trenchard had mentioned some recent sinkings of ships to the Doctor, and when Robbins (Royston Tickner), the boatman who ferried him and Jo out to the island, mentions it as well, the Doctor goes to investigate a charred lifeboat which was found and taken to HMS Seaspite, a nearby naval base. 

At the base, Captain John Hart (Edwin Richfield), and his secretary, 3rd Officer Jane Blythe (June Murphy), are also concerned with the sinkings, the most recent of which was the SS Pevensey Castle. Blythe sees the Doctor looking at the charred lifeboat from the window; he is arrested and taken to see Hart. Hart eventually believes he wants to help when Jo arrives with the UNIT passes. 

Both the Doctor and the Master arrive at the conclusion that an abandoned sea fort, which is mid-way between the final locations of the sunk ships, may hold a clue to what is happening. The Doctor and Jo make their way there to find Hickman (Hugh Futcher), one of two caretaker workmen, dead, and the other, Clark (Declan Mulholland), insanely raving about sea monsters. Also on the fort is a humanoid lizard-like creature (Pat Gorman) and one of these creatures destroys their boat. The Doctor sees the creature and manages to scare it off with an electric shock, before using an adapted transistor radio to signal for assistance. Hart has already called for air-sea rescue when the Doctor and Jo cannot be found on the island and have not arrived on the mainland, and the Doctor and Jo are lifted from the fort. 

The Doctor believes these creatures to be acquatic relatives to the ones he met under Wenley Moor in Derbyshire, which had been incorrectly called Silurians; they should have been called Eocenes. Back at Hart's office, Jo sees the Master from the window dressed as a Naval Officer. Trenchard has brought the Master to the base to obtain some electronic spares. The Doctor and Jo return to the prison where they discover that the telephones are apparently dead. Jo leaves to try to alert UNIT and to have Trenchard and the rest of the prison staff replaced while the Doctor goes to see the Master. They fight with swords and the Doctor wins. However, Trenchard has him locked up. The Master explains to the Doctor that he intends to help the reptiles to rule the Earth once more. Blythe reports that the Doctor and Jo have again gone missing and Hart visits the prison after ordering Commander Ridgeway (Donald Sumpter) to take a submarine fitted with an experimental sonar to inspect the sea bed at the base of the fort. 

In the distraction caused by Hart's arrival at the prison, Jo frees the Doctor and they escape to the beach. There, the Master uses a calling device that he has built to summon a reptile from the sea. It chases after the Doctor and Jo but they escape though a minefield, the Doctor detonating some mines behind him with his sonic screwdriver to send the reptile back into the sea. 

Meanwhile the submarine's engines fail, it sinks to the sea bed, is attacked and boarded. The reptiles take the submarine to their base. 

The Doctor and Jo try and warn Hart about the reptiles. He won't believe them but agrees to help. The Doctor takes a diving vessel, HMS Reclaim, out to the fort and is lowered to the sea bed in a diving bell. He sees a reptile in the water. When the bell is returned to the surface, the Doctor is missing. 

The Master again summons the reptiles (Marc Boyle, Peter Brace, Alan Chuntz, Jack Cooper, Stuart Fell, Pat Gorman, Bill Horrigan, Mike Horsburgh, Steve Ismay, Brian Nolan, Frank Seton, Mike Stevens, Terry Walsh, Derek Ware, Geoffrey Witherick), this time to attack the prison. They kill Trenchard and rescue the Master. 

In the reptiles' base, the Doctor tries to persuade their leader (Peter Forbes-Robertson) to seek peace. The Master, who is also present, warns that the humans intend death to them all and wants the Doctor to be destroyed. Just as the Doctor is winning the argument, the Navy begins dropping depth charges on the order of the Parliamentary Private Secretary, Walker (Martin Boddey), and the reptile reader has the Doctor taken to the cells. The Doctor escapes and releases the submarine crew. They all escape in the submarine. 

The reptiles want the Master to revive the rest of their people, but to do so the Master needs more electronic spares from the naval base. He arranges for the reptiles to attack the base and the Doctor and Jo are recaptured, along with Hart. The Master wants the Doctor to help him revive the reptiles and the Doctor agrees to construct a sonar device, similar to a laser, to pinpoint their bases. The Doctor manages to create a diversion and Jo and Hart escape in a hovercraft. Hart returns with reinforcements to try and defeat the reptiles. The Master escapes out to sea in a small jet-boat and the Doctor follows. They are both recaptured by the reptiles and returned to the underwater base. 

The Master connects his device into the reptiles' power system, but the Doctor reverses the polarity of the neutron flow which will result in a massive explosion. At the same time Walker requests a nuclear strike on the underwater base. The reptile leader has the Doctor and the Master locked up, but they escape from the cell and head for the surface where they are picked up by a hovercraft just as the reptiles' base explodes. 

The Master manages to escape by feigning an illness and then hijacking the hovercraft once the Doctor has left.

_{Synopsis from Doctor Who: The Third Doctor Handbook by David J. Howe, Mark Stammers and Stephen James Walker, reprinted with permission; further reproduction is not permitted. Available from Telos}