The TARDIS is drawn off course by Anzor, a school bully who tormented members of the Doctor's class at the Academy. He orders the terrified Doctor to engage his own TARDIS' trans-replicator mode and switch places with him, and the Doctor does so only to find that his TARDIS is now being held captive by an alien spacecraft which is bombarding the planet Magnus Epsilon with radiation. Anzor, meanwhile, completes his journey to the planet's surface, where is greeted by the planet's ruler, Rana Zandusia. An air-borne virus on Magnus Epsilon causes death to all males exposed to sunlight, but the female rulers of Magnus fear that their neighbours on the planet Salvak have found a cure and intend to invade. The Magnii have therefore made a deal with the Doctor's old enemy Sil to summon a Time Lord and put their case to him; they wish to travel back in Time, prevent the discovery of the virus, and thus stop the war before it starts. Anzor refuses to grant permission to change history, but before he can depart, the Magnii use a control ring to hypnotise him, intending to extract information on time travel from his brain.

The Doctor manages to escape when the spaceship's force field is weakened by its constant bombardment of the planet. The TARDIS materializes in the tunnels beneath the Rana Zandusia's palace, where Peri and the Doctor are greeted as saviours by a group of rebel boys who have escaped from the Magnii's breeding colonies. A patrol of matrons searching for their errant charges encounters the Doctor, and they use their control rings on him, forcing him back to the palace to be questioned by the Rana Zandusia. Most of the boys scatter in panic, but their leader, Vion, agrees to take Peri to the palace to search for her friend. Upon arriving, Vion is captured by the matrons, who sentence him to death for breaking curfew. Peri follows and rescues him, and in the process gets her hands on one of the matrons' electric stun-rods; she and Vion now have a weapon.

The Doctor is taken to the telepath Ulemi, who attempts to read his and Anzor's mind as Zandusia watches. They are apparently able to block her attempts, and while exhausted from the effort Ulemi babbles about Zandusia's greed for power. Zandusia assumes that the Doctor is forcing her to say such things in order to undermine her authority, but when the Doctor recovers he informs Ulemi that in her weakened state she spoke what she truly believed. Ulemi, however, can't accept this and reports to Zandusia that, while the Doctor was bombarding her mind with useless information, she slipped beneath his defences and took all she needed to know about operating the TARDIS. The Magnii force Anzor to open his TARDIS, and upon seeing him humiliated before them, the Doctor finally loses his childhood fear of the bully. The Magnii programme Anzor's TARDIS using the information copied out of the Doctor's mind, but before they can dematerialize, Anzor overpowers them and drives them out. He forces out the Doctor as well, intending to return to Gallifrey and report that the Doctor has surrendered the secrets of time travel, but as he departs, the Doctor admits that he tricked Ulemi and allowed her to take false information from his mind. Anzor's TARDIS is now fixed on a locked-off journey, travelling very slowly back to the dawn of creation, and the Doctor doesn't believe that Anzor has the knowledge to alter his course.

Zandusia, accepting this evidence of the Doctor's deviousness and intelligence, tries to win him over to their side, explaining that the Salvakans have already begun to melt the polar ice caps in preparation for their invasion. The Doctor, however, refuses to grant them access to his TARDIS, especially as they're in league with Sil; he's convinced that Sil intends to betray them and begin mass-producing time machines once he has access to the Time Lords' technology. As the Magnii begin trying to break into the TARDIS, Peri and Vion arrive and rescue the Doctor, and they flee towards the ice tunnels of the north in order to investigate the climatic changes which Zandasiua had described. Zandusia, meanwhile, ponders the Doctor's warnings and questions Sil about his recent construction of factories; he seems to be producing large quantities of heating devices and cold-weather apparel, and yet Magnus is a warm, balmy planet. Sil claims that he was planning to export to Salvak, and the amused Zandusia, knowing that Salvak is even warmer than Magnus, dismisses the matter as trivial -- unaware that Sil is lying to her. The Magnii finally manage to break into the Doctor's TARDIS, but in his joy, Sil accidentally operates the wrong controls and sends the TARDIS a few hours ahead in time -- and the scanner screen shows an image of devastation. In the past few hours, the planet has been all but destroyed...

The Doctor, Peri and Vion reach the ice tunnels, where they find a nuclear device capable of destroying all life on Magnus Epsilon, and are then attacked by an Ice Warrior. Peri is captured and taken to the Ice Lord Vedikael for interrogation, and she bargains for her life by offering to serve them. She is thrown into prison with the four survivors of the Salvakan spearhead, who were taken prisoner after their ship was shot down by the Ice Warriors. The Ice Warriors are using them as slave labour, to hollow out further ice tunnels and plant nuclear devices in them. The Doctor and Vion locate the Ice Warrior camp, but their attempt to rescue Peri and the Salvakans and to disrupt the Ice Warriors' base is only half-successful; they manage to escape, but two of the Salvakans are killed in the process. Realizing what the Ice Warriors intend to do, the Doctor sends the others to shelter while he attempts to return to their base and disrupt their plans, but he is too late; the nuclear devices in the tunnels go off in sequence, and Magnus Epsilon is knocked into an orbit further away from the sun. The climate will now change to perpetual winter, and Magnus Epsilon will become the Ice Warriors' new home.

The Doctor, Peri, Vion and the Salvakans return to the tunnels beneath the Magnii's palace, where they find a shattered Ulemi weeping for the destruction of her home. The TARDIS returns, and when the Magnii emerge, a cackling Sil reveals that he has been in league with the Ice Warriors all along and will now make a fortune selling his cold-weather supplies to the Magnii. A patrol of Ice Warriors arrives to capture the Magnii and Salvakans, and in the confusion Sil's bearers are shot dead and he orders the Doctor and Peri to take their place. They are forced to carry Sil to the Ice Warriors' base, where the Ice Warriors are setting up a sonic burner to clear all indigenous life forms out of the tunnels. The Ice Warriors announce that they no longer require Sil's services and that he is therefore to be killed, but as Sil sputters apopleptically, the Doctor manages to escape and turn the sonic burner on the Ice Warrior guards, killing them.

Sil, infuriated by this betrayal, reveals that the Ice Warriors have set up a second system of bombs in case the first network failed. The Doctor detonates them, changing the planet's orbit once again, but he, Peri and Sil are then captured by more Ice Warriors before he can be sure whether he's solved matters or made them worse. They are marched to the ruins of Zandusia's palace, where Zandusia herself, her fellow Magnii and the Salvakans are all awaiting execution. But as the Ice Warriors line up to form a firing squad, the climate of the planet returns to normal, and Vedikael and his warriors perish from the heat before they can execute their prisoners. Magnus now requires rebuilding, and the Salvakans offer their assistance as husbands to the Magnii. The Doctor and Peri depart, while Sil plans to get rich selling matrimonial and baby goods to the Magnii and Salvakans.