Stockbridge's resident harmless lunatic, Maxwell Edison, locates what he believes to be an alien spacecraft with a dowsing rod.  While trying to track it down in the darkness of Wells Wood he stumbles into the TARDIS and meets the Doctor, who is surprised to learn that an alien ship really is approaching the Earth.  He takes Max to the alien ship, which appears to be derelict and deserted, but Max becomes convinced that a malevolent entity is prowling the corridors.  When the Doctor breaks into the ship's bridge he inadvertently releases an intangible force which appears to dissipate into thin air.  Concluding that the ship had evolved a life force of its own over millennia of abandonment, the Doctor takes Max back to Stockbridge, where Max earns a little grudging respect when he successfully predicts a spectacular meteor shower -- the result of the alien ship breaking up in the Earth's atmosphere.

The Doctor's holiday in Stockbridge is interrupted yet again when he learns that an imprint of a London police box has been found in millennia-old limestone at the local quarry.  He soon confirms that the imprint has come from his TARDIS, but before he can investigate further he is attacked by an elemental being, a force formed of fire and fear.  He attempts to escape into deep space, but the being breaks into the TARDIS and possesses the ship.  The Doctor sends a distress call to Gallifrey, and Shayde is sent to help while a military TARDIS commanded by Tubal Cain -- a conservative Time Lord who detests the Doctor's revolutionary personality -- stands by to destroy the Doctor's TARDIS at the first sign of trouble.

Shayde enters the datascape of the TARDIS computers and manipulates the energy being into the Matrix, where it will be content at last.  The Doctor then dematerializes the damaged TARDIS, and Cain, caught off guard, fires a salvo of time torpedoes at him -- and realizes too late that the Doctor has travelled to Gallifrey's military base.  The torpedoes detonate above the base before the TARDIS materializes, freezing the base in Time, and thus giving the Doctor weeks to conduct repairs while no time passes outside his ship.  When the time warp breaks, he is arrested and charged with releasing into Earth's history the elemental being from the ship which he and Max Edison discovered.  The force from the ship possessed the TARDIS and took it back to prehistoric Earth, and the TARDIS then returned to the 20th-century, leaving the energy being stranded and alone.  The Doctor is thus responsible for all the death and destruction caused by the being as it journeyed through history, seeking the TARDIS again.  But Shayde, for reasons of his own, destroys the imprint of the TARDIS in the Stockbridge quarry, and as they have no evidence to prove their case the Time Lords are forced to release the Doctor.

Trying to relax after his trial on Gallifrey, the Doctor travels to a South Pacific island to try his hand at fishing.  Although he believes it to be 1983, he is nonetheless captured by a Japanese soldier named Fuji who insists that the war is still being fought.  Fuji claims to be an advance scout sent to survey the island for his unit, but when an aerial dogfight breaks out over the island -- proof that the fighting has already reached this area -- the Doctor realizes that Fuji is in fact a deserter. Fuji is injured when an American bomber strafes the island, and the Doctor attempts to nurse the frightened, confused young fisherman back to health; but Fuji, delirious, rejects his help and stumbles off into the forest, determined to prove that he is a proper soldier.  An American soldier has been shot down and parachuted to safety on the island, and when the two soldiers meet, Fuji shoots first.  But the Doctor, worried about Fuji's instability, had removed the bullets from his gun earlier, and the American soldier shoots Fuji dead.

The Doctor is held at gunpoint by an American pilot, but on hearing his accent the pilot assumes him to be British secret service. The Doctor is puzzled that a war he thought was long over is still being fought. When the pilot tells him it is 1963 he realizes he is on a parallel world and in a sudden mood of confusion, feeling adrift in time, the Doctor stumbles into the sea. Not being able to swim, he has to be rescued by the pilot who takes him to the TARDIS and is naturally astounded by its interior dimensions. The Doctor offers him a way out of the war, though he hints darkly that the time travel he is offering could be more dangerous.

The pilot, introduced as Angus ‘Gus’ Goodman, is taken on a trip across the wonder of the universe. Back near Earth the Doctor tells him about the existence of countless parallel universes. Below them, at that moment, a British airliner is shot down by a beam of energy above the Arctic Circle. It has come from a gun fired by an ice warrior but provided by a renegade Time Lord. There is an Ice Warrior base in the snowy wastes, protected by a temporal shield (which caused the parallel worlds that so confused the Doctor). The Doctor manoeuvres the TARDIS through the shield and lands on the snow only to take a direct hit from the energy beam. He immediately dematerialises.

At the same time a supersonic aircraft takes off from a secret base in Scotland, part of an operational unit known as SAG 3. It flies to the Arctic and drops a probe. As the long Arctic night closes in the TARDIS rematerializes and the Doctor and Gus trudge to a ridge where they see the Ice Warrior base. They hitch a ride on a passing motorized sledge and find themselves deep within the base. They see that the Warriors are dropping something down a deep shaft into the ice. The sudden materialization of a TARDIS by the shaft makes Gus cry out. A guard shoots at him with a sonic canon and the Doctor is hit by flying rock fragments. Gus flees out of the base but the Doctor is captured.

It transpires that the renegade Time Lord is the Time-Meddler. The Doctor drops a device down the shaft that removes the temporal shield. Outside, Gus meets three SAG 3 men, highly trained soldiers with a telepathic bond. These three eliminate the perimeter guards and infiltrate the Ice Warrior base. They see the Doctor suspended over a pit. The Ice Warriors shoot and injure one of the men but as they close in on the others the Ice Warrior leader, Autek, orders the launch of his ship. This is, it turns out, the top of the base, and its launch incinerates the Ice Warrior ground troops. The SAG 3 men shoot the Doctor’s bonds to save his life and Autek and the Time Meddler use a TARDIS to travel five million years into the future.

On board his own TARDIS the Doctor tells the SAG 3 men that the Ice Warriors were dropping super heated silica down the shaft. Cooling this over millions of years creates huge crystals that can be used to make a sonic canon capable of erasing a whole continent. The Doctor reveals that his whole mission to Earth was a voluntary one, instigated by his 'superiors', to investigate this possibility. SAG 3 was simultaneously coming to similar discoveries. With some adept flying the Doctor chases the Time Meddler back to the Ice Warrior mother ship and materializes in the same place, but a micro-second earlier. This blasts the Time Meddler into another dimension and destroys the space craft and its deadly weapons. Returning the SAG 3 men to their base the Doctor declares his time on Earth is done, he just needs to get Gus home.

The Moderator is cruising the galaxy with a cool million in platinum ingots from Intra-Venus Inc, instructed to track down the TARDIS. He casually wastes exotic life forms and temples while the same tune is playing over and over in his head.

Earlier, the Doctor and Gus land on a planet called Celeste where a group of high-tech soldiers called Gaunts pursue them for breaking curfew. They only just escape in time down a tunnel that leads underground. Celeste is a mining planet owned by the mega-rich entrepreneur J.W. Dogbolter, half man-half frog, the most evil being in the universe. He is here to supervise the putting down of a revolt by the Moles, men who work Celeste’s ruby mines. His prime weapon is a combat robot called The Wrekka. Unfortunately this robot, armed with 300 weapons, is also brain damaged. However, it still tracks down the Doctor and Gus and arrests them as ring leaders of the revolt. When the Doctor admits he arrived in a time machine Dogbolter’s greed is aroused. It is revealed that the Moles are Intra-Venus company men who have displeased their boss. During the Doctor’s interrogation the Moles attack Dogbolter’s offices, allowing the Doctor and Gus to retreat to the TARDIS. This is when the Moderator is called in.

Three weeks later he finally tracks the TARDIS to Earth just as the Doctor is dropping off Gus. He makes an attack, running across the sand and shooting Gus who manages to return fire, Three bullets hit the Moderator, whose armour is made to deflect high energy weapons, not lead bullets. As he falls he realizes that the song that has been plaguing him was “We'll Meet Again”, jammed on repeat on his headset. Gus dies and the Doctor picks up his gun and puts a bullet into the headset before leaving. The seriously injured Moderator is taken to hospital where he is given a private ward. There he is visited by Dogbolter’s aide, Hob, who switches off the life-support system as payment for the Moderator’s failure.

The Doctor detects a source of alien energy from Earth's moonbase in the year 2015, and materializes to investigate. A technician named Jeffries has just returned to the moonbase with two visitors -- cows in spacesuits, who identify themselves as Vartex and Ravnok of the Dryrth species, and who request time to rest while their crashed spaceship repairs itself. The suspicious Tegan and Turlough locate the source of the alien energy which drew them here, a canister buried beneath the Moonbase, and notice that the markings on the canister match those on the Dryrth's spacesuits. The two Dryrth are in fact vicious criminals who kill Jeffries when he finds them trying to break into the Moonbase reactor. They hold the Doctor hostage while Ravnok sets the reactor to overload, explaining that they must blow up the Moonbase to recover the treasure buried beneath it. The Dryrth are normally a peaceful species, but Ravnok released a plague to improve their moral fibre and was thus sentenced to three thousand years' imprisonment. Commander Jackson shoots Vartex and forces Ravnok to retreat, but once out on the lunar surface Ravnok finds that Jackson had sabotaged her oxygen supply, and collapses before she can reach her ship. The Doctor stops the reactor from overloading and then informs Jackson that the "treasure" was in fact a canister full of cheese, the basis of the Dryrth economy.

The Fifth Doctor and Peri materialize on a studio backlot in 1930s Hollywood, where eccentric director Seth Rakoff is filming a movie with Raschid Karnak as the Mummy. The film is running over-budget, and producer Monroe Stahr threatens to remove Rakoff from the project; but the Doctor is more concerned with the fact that the sarcophagus at the centre of the set is the genuine Scarabaeus, which according to legend holds the beetle-god Kephri. Stahr is killed while watching rushes of the day's work, and his internal organs are removed. The Doctor and Peri, meanwhile, enter the pyramid prop to find it filled with Osirian technology, including the mummy robot which killed Stahr. Karnak is waiting for them there, to tell his story; he is dying, his body eaten away from within by the curse of Kephri. Rakoff hired him as a guide in Egypt and took him to the tomb described in the grimoire of Anubis, where Karnak fell under the spell of Kephri and was forced to accompany Rakoff and the contents of the tomb to America.

Rakoff shoots and kills Karnak, telling the Doctor that in Hollywood, nobody will even notice that he's casting a spell to raise Kephri. He casts a spell which brings the extras -- and Peri -- under his psychic control, and forces the Doctor to complete the ceremony which will raise Kephri. The Scarabaeus turns out to be empty; Kephri has already entered Karnak's body and has been feeding on him for months. Peri removes the ankh around Karnak's neck, restoring Kephri to full power, and the scarab god releases a plague of locusts which consume the greedy Rakoff and prepare to devour the Earth. Before they can do so, the Doctor holds the ankh in front of a studio light, casting its shadow over Kephri; he then orders one of the Osirian robots to seize the totem, and the robot rips Kephri apart trying to seize the shadow. The Doctor and Peri depart, but the Doctor is unaware that earlier, while alone on the lot, Peri was removed and then returned by someone -- or something...