The year is 2084, and Earth is divided into two hostile blocs which eye each other suspiciously for the slightest wrong move, armed with proton missiles which could destroy all life on Earth while leaving the planet itself intact. But there are other forms of life on Earth... A Silurian battle cruiser lands near a Sea-Devil hibernation chamber near one of the human blocs' Sea Bases, and when an inquisitive probe is launched the Silurians release a "Myrka" to destroy it. The crew of the Base aren't sure how to react to the probe's destruction, as their sensors are picking up nothing but marine life. The base's temporary synch operator, Maddox, whose job it is to link to the computer in times of crisis, is unprepared for the emergency; he's only a student thrust into this position by the accidental death of the base's former synch op, Michels. Maddox's friend Karina talks him back to work, unaware that his suspicions about Michels' death are justified; the base's second-in-command and doctor, Nilson and Solow, are enemy agents who murdered Michels in order to put the unstable Maddox in a position where they can use him...

Turlough, for reasons of his own, has decided to remain aboard the TARDIS. The Doctor materializes in orbit around Earth in order to show Tegan some of her planet's future, but they are shot down by a satellite defense system and the Doctor is forced to make an emergency materialization on the Sea Base. Their encounter with the satellite having coincided with the destruction of the Base's marine probe, the Base's computer triggers what could be a missile run. Maddox is forced to synch up to the computer in preparation for what could be the first strike of the last war. The run turns out to be a simulation to test the crew's battle readiness, but the stress causes Maddox to pass out, and he is taken to the psychosurgical unit for care. With Maddox incapacitated the Base is defenseless...

The Silurians, meanwhile, have docked with the hibernation chambers near the Sea Base, and are preparing to revive the Sea Devil patrol there. As the Silurians Scibus and Tarpok activate the revival circuits, Ichtar -- the sole survivor of the Silurian Triad -- waits patiently. The process will take some time, and the long period of hibernation may have caused the Sea Devils' muscles to atrophy; all they can do is wait...

Nilson and Dr Solow call Commander Vorshak to the PS unit to report that Maddox is on the verge of a complete mental breakdown. The Base is under strict orders to maintain radio silence to avoid giving away its location to the enemy, and Vorshak is thus unable to contact Sea Base Command for advice. He thus reluctantly authorises the release of Maddox's spare conditioning disc, and hands it over to Nilson and Solow with orders not to let it fall into enemy hands. Theoretically, Solow can now delve into the depths of Maddox's mind and remove the deep-seated inhibitions which prevent him from doing his job. But instead, she programmes him to obey her and Nilson's every command...

The Doctor recovers and swims to safety, emerging through an airlock hatch in the bottom of the pool. Turlough and Tegan sabotage the lock to the reactor room and flee, and a soldier sent to repair the lock is knocked out by an electrical discharge. The Doctor finds the unconscious soldier and takes his uniform in order to move freely about the Base. Turlough is captured and taken to the bridge for questioning, but Tegan is reunited with the Doctor and they set off for the bridge to rescue him. Nilson and Solow aren't sure who the intruders are, but the distraction may give them the chance they need to activate Maddox...

The Sea Devils are successfully revived, and immediately orient themselves for battle readiness. Ichtar gives the patrol leader, Sauvix, a detailed plan of battle. They must take the ape-primitives' base intact.

Turlough tells his story to Vorshak, who isn't sure what to make of it. Nilson suggests sending Turlough to the PS unit for mind-probing, but the Doctor slips onto the bridge, surprises a soldier and takes his gun. But instead of using it he hands it over to Vorshak to demonstrate his good intentions. Preston, meanwhile, locates the TARDIS and is shocked by the size of the interior, which would seem to confirm Turlough's story. On her way back, she locates Tegan and takes her to the bridge as well. Vorshak is now willing to listen to the Doctor, but they are interrupted by the approach of the Silurian battle cruiser. The Doctor, recognizing it for what it is, urges Vorshak to contact the Silurians peacefully, but Vorshak orders his crew to open fire and drive the vessel away. The blast is reflected back at the sea base, knocking out its exterior weapons, and the Doctor realizes that, like it or not, he's once again on the wrong side in a war between the Earth's two intelligent species.

The Silurians dock with the Sea Base, and begin breaking into airlocks One and Five. Preston and Vorshak go to Five with a detachment of soldiers while the Doctor, still hoping to make peaceful contact, accompanies Bulic to airlock One. Nilson is left in charge on the bridge -- and seizes the opportunity to activate Maddox, using a hand-held device to trigger a seizure and summoning Solow to "help" him. Solow takes Maddox into the computer bay for treatment, but Karina is suspicious and enters the bay when Nilson isn't looking. There, she finds Solow watching as Maddox pulls apart the missile launch computers and communications equipment. Nilson arrives and orders Maddox to strangle Karina to death, and Maddox has no choice but to obey...

The Doctor throws a power pack from a soldier's gun at the Myrka, and the pack explodes as soon as it hits the creature's electrically charged skin, temporarily blinding it. Bulic leaves one soldier on guard and takes the others to Airlock Five, but Turlough rushes to the bridge and holds Nilson at gunpoint, ordering him to lift the bulkhead. Nilson does so, but as the Doctor and Tegan flee, the remaining soldier gets too close to the Myrka and is electrocuted. The Myrka then holds an arm in the way of the closing bulkhead, blowing out its hydraulic valves, and enters the base, killing everyone it encounters.

The Doctor and Tegan warn Vorshak of the danger, and although Vorshak is furious with Turlough he has no choice but to let the Doctor try to deal with the situation. Preston accompanies the Doctor to provide him with the authority he needs to requisition equipment. Moments later, the Sea Devils burn through the airlock seals and march into the Base, slaughtering the human defenders. The humans retreat and seal the bulkheads, but the Sea Devils immediately begin to burn their way through. Turlough arrives in search of the Doctor and Tegan, and Vorshak and Bulic force him into the front lines. Vorshak now has no choice but to break radio silence and warn Sea Base Command about the danger. He calls the bridge and orders Nilson to prepare Maddox for synch-up, and Nilson sends Solow to wait for him at the escape pod while he forces Maddox to work faster.

On the Doctor's instructions, Preston fetches an ultraviolet converter from the Base's solarium, and the Doctor sets it up in a corridor in the path of the Myrka. He intends to use it to boost the lighting to a level which the Myrka, a creature adapted to the depths of the ocean, will be unable to tolerate. Solow rushes past, ignoring their warnings, and runs straight into the Myrka, which kills her. As the Myrka continues on its way, two soldiers find Solow's body -- and discover that she was carrying Maddox's conditioning disc. Vorshak is checking on the Doctor's progress when the soldier Paroli brings the disc to him, and, concerned, the Commander takes Preston with him to the bridge to question Nilson. The Doctor completes his work just as the Myrka comes into view... and as it approaches, the Doctor switches on the converter and floods the corridor with ultraviolet light. The Myrka instantly drops dead.

The Sea Devils break through the bulkheads, and steadily drive back the human defenders. Ichtar and the other Silurians are soon able to join their Sea Devil forces on the Base, where they detect the death of the Myrka and order Sauvix to divert his forces and capture the bridge. Soon Bulic, Turlough and Paroli are the only defenders left alive -- until they find themselves trapped between two Sea Devil patrols and Paroli is shot and killed. Bulic and Turlough have no option but to surrender, and they are taken to the crew quarters to await their fate as the Silurians and Sea Devils head for the bridge.

The Doctor and Tegan are taken prisoner and returned to the bridge, which is now under Silurian control. Tegan and Preston are taken to the crew quarters, but the Doctor, recognising Ichtar as the sole survivor of the Silurian Triad, identifies himself and demands an explanation. He is horrified by the answer; following their earlier betrayals at the hands of humans, Ichtar has abandoned the ways of peace and now intends to commit genocide. The Silurians intend to launch this base's proton missiles into space; although they will have killed no-one but this base's defenders, in the paranoid atmosphere now prevalent on Earth, the launch will trigger a war which will wipe out humanity. The Silurians quickly repair the damage Maddox caused and use a Manipulator to replace the missing synch operator. They still require Vorshak's handscan to bypass certain security precautions, and the Doctor advises him to co-operate for the moment and await his chance to take action.

Turlough manages to open a ventilation shaft in the crew quarters through which the prisoners can escape, but while he intends to return to the TARDIS, Tegan and Bulic insist upon first rescuing the Doctor and Vorshak. They manage to get to the computer bay and contact the Doctor, who slips away while his guards are occupied watching the preparations for launch. Meanwhile, Preston shames Turlough into returning for his friends, and, reunited, they set off for the chemical stores. There, they are attacked by a lone Sea Devil which accidentally shoots open one of the Hexachromite canisters. The pressurised gas causes the Sea Devil's skin to melt away on contact, but the Doctor refuses to use this as a weapon -- if only he has the time to find something less lethal...

Sauvix discovers that the prisoners have escaped and that the Doctor is also gone. Ichtar had intended to allow the Doctor to leave peacefully once the launch was complete, but instead decides that he's too dangerous and orders Sauvix to find and kill him. The computer triggers a simulated missile run, but the Silurians use the Manipulator to convert it to a real launch procedure. As the base enters yellow alert, the Doctor realizes that he's run out of time, and reluctantly prepares to pump Hexachromite into the Base's air ducting to force the Silurians to retreat. Before he can start the pump, however, Sauvix locates him and orders him to shut it down. Sauvix shoots Preston dead as she goes for her gun, but Bulic then grabs a canister of Hexachromite and kills Sauvix. The Doctor takes Tegan and Turlough to talk sense into Ichtar, leaving Bulic to operate the pump -- but Bulic simply loads canister after canister into place, and as the Doctor heads for the bridge he realizes that the Base is filling with the gas too quickly for the Silurians to escape.