In the distant future at Brittanicus Base, senior control technician Jan Garrett and her staff struggle to control an ioniser which they are using to slow the progress of glaciers rolling over Britain. Leader Clent is convinced they will be able to avert a new Ice Age but the group knows they are only a few hours away from being forced to abandon the base. Tensions rise when Penley, a maverick scientist who has defected from the team, is mentioned. The remaining senior scientist, Arden, is out on the glacier searching for archaeological finds, where he discovers an armoured man within a block of ice. Arden and his colleagues ignore appeals to return to Base and help Clent control the Ioniser, intent instead on digging the ice man from the glacier. Two scavengers observe their actions: the anti-technology Storr and Penley, who both live in the tundra away from technology. When one of Arden’s team is killed in an avalanche, the other two head back to base with the ice man. Storr too is injured in the avalanche, breaking his arm.
The TARDIS arrives outside the base. The Second Doctor, Jamie and Victoria go inside, where the Doctor offers to help with the Ioniser. His action saves the Ioniser and coupled with his scientific analysis of the current ice age – that it has been caused by a severe drop in the carbon dioxide level of the atmosphere following the wholesale extermination of plant life – Clent is persuaded of his usefulness, despite initial misgivings.
Arden and Walters reach the base with their prize, and Arden sets up a device to melt the ice around the man. The Doctor examines the frozen man; as the creature’s helmet incorporates electronic parts, they determine that the "ice warrior", who has been entombed since the last ice age, is an alien being. Minutes later, an emergency meeting distracts the staff; no-one notices that the ice block has completely melted, with the creature showing signs of life.
The creature becomes mobile, knocks Jamie unconscious and takes Victoria as a hostage.
The ioniser planning meeting is interrupted by the Doctor’s news about the warrior. He concludes that if the creature is indeed alien then there could be a spaceship under the glacier which could be powered by atomic systems; using the ioniser in that area could cause a massive explosion that would destroy the Base. The crew are discussing this when Jamie bursts in and reports the creature has come to life and taken Victoria. An alert is issued throughout the base, but only Arden and Jamie can be spared for a search party.
The creature identifies itself to Victoria as Varga, an Ice Warrior from the planet Mars, who has indeed been frozen for millennia. He insists Victoria help him find his ship and crew; with the extra troops he can decide whether to return home or stay and conquer the Earth. Varga steals power packs from the medi-centre to revive his crew.
Penley has meanwhile helped Storr back to their hideout, where Storr’s injuries are determined so bad that Penley needs to go back to the Base to steal some medical supplies. He sees Varga and Victoria in the medi-centre and follows them as they leave the Base. They encounter Clent before leaving, and Varga leaves him unconscious and badly wounded. Penley tries to revive Clent and is found doing so by the Doctor, who has worked out he is the errant scientist. Penley, once sure the Doctor is dealing with Clent, leaves the Base, despite’s the Doctor’s protests that he is needed to help with the Ioniser. When Jamie and Arden return from their search, the Doctor persuades them that with the prospect of more than one creature buried in the glacier they should play for time. They postpone the next phase of the search until morning.
Meanwhile, in the glacier, Varga finds four of his frozen comrades and prepares to revive them.
Varga begins the process of reviving them, which takes all night. His lieutenant, Zondal, is given the task of creating defensive structures in their ice cave while the other Ice Warriors set about finding their missing craft and digging it out of the ice. Varga is observed by Penley, who is back tracking in the snow having used the medicine on his friend Storr. When Penley returns to Storr he is surprised to find a visitor, Miss Garrett, who implores him to rejoin the crew of the Base at this critical time. When other approaches fail, she tries to take him at gunpoint but Storr intervenes. Miss Garrett is sent away with Penley’s advice to “check the Omega Factor”. The Doctor tests the new data in simulation mode and proves that the Ioniser can be used more effectively.
Back at the Base, Jamie and Arden are sent into the glacier, ostensibly to find the alien spacecraft rather than Victoria. They discover the Ice Warriors’ cave excavation and report this back to Base. Minutes later, they are ambushed and gunned down by the Ice Warriors, who leave them for dead. Penley investigates and finds Arden has indeed died, but Jamie is still alive. Penley decides to take him back to his home. Storr decides to speak to the Ice Warriors himself, convinced they might be potential allies. Penley heads after him, warning of their ruthlessness.
Having failed to contact Arden, the Base personnel assume something bad has happened. Moments later, the video link comes alive, operated by Victoria, who tells them of the danger of the Ice Warriors. She is probed by Clent about the propulsion system of their ship. Zondal, concerned that Victoria will reveal their location, trains the ship's weapons on Victoria.
Varga stops Zondal, in order to evesdrop on Victoria's conversation and learn the Base's primary concern, and to use it as a weapon against them. An Ice Warrior is sent to capture Victoria again and use her as bait. The Doctor decides to go to the spaceship and rescue Victoria. Before leaving, he takes with him a phial of ammonium sulfate, which he deduces will be noxious to aliens from a nitrogen based atmosphere such as Mars. However, Victoria flees ever deeper into the icy caves. When the Ice Warrior, Turoc, finds her he is caught in an avalanche and crushed – with Victoria alive but trapped in his dead claw.
An examination of the engines of the Martian craft reveal them to be functional but low on fuel. When the Ice Warriors encounter Storr they ignore his offers of help, especially so when he denounces scientists at the very time they want technical aid. Storr is killed but Victoria, who he brought from the ice caves, is permitted to live.
Meanwhile Penley has found the Doctor and taken him to Jamie. He determines Jamie’s paralysis is temporary and heads off to the Martian craft. Once there he offers himself as an envoy, leaving his communicator active so Clent can hear, and is allowed to enter the airlock. Varga, suspicious of the Doctor's claims, reduces the pressure in the airlock to zero until the Doctor explains his motives.
Seconds away from death, the Doctor agrees to Varga's demands. With the glacier threatening to crush the spacecraft, the Doctor succeeds in getting Victoria released to him. He is less successful in persuading Varga that the Ioniser is anything but a weapon that could be used against the Martians. The last thing the Doctor is able to establish before Varga takes the communicator is that Clent needs to use the Ioniser at some point, regardless of consequences. The Doctor is marched to the core of the spacecraft, where he spots an ion propulsion system. Varga decides to attack the Base before the Ioniser can be used, and orders his Warriors to prepare a sonic cannon.
Penley has brought Jamie to Base on a motorised sled. Clent gives Penley a frosty reception, and they end up bickering. Clent says he has decided to adopt the Doctor’s advice and use the Ioniser, even if the computer seems unconvinced of the merits of such a proposal. The Doctor and Penley’s new formula for ionisation has been tested in other Bases with great success and is scheduled for use in Britannicus in a few hours time.
Zondal has been given the task of arming the sonic cannon. With Varga and his other Warriors, Isbur and Rintan, focussed on this attack, the Doctor and Victoria use the opportunity to release the chemical solution in Zondal’s face. The Warrior collapses, but his hand activates the sonic cannon as he falls.
The sonic blast triggered by Zondal only glances the Base, causing minor damage. Varga uses the communicator to call Clent, threatening to fire again unless the humans surrender. Clent knows the Base dome cannot survive another sonic blast and suggests a peace meeting between the two sides. The Ice Warriors confront the humans in the Ioniser room. The talks fail when a demented technician, Walters, tries to shoot the Martians. Varga dismantles the Ioniser reactor to get the mercury isotopes he needs for his ship, not caring how this will affect the humans and the Dome. Without the ioniser, the glaciers begin to move forward.
The Doctor and Victoria adjust the Martian sonic cannon so it will harm the Ice Warriors and not the humans. Similarly, Penley, who was not in the Ioniser Room, alters the temperature and atmosphere controls in the Base so it becomes uncomfortable for the Martians. The Doctor fires the sonic cannon, forcing Varga and his men to retreat from the Base. He fuses the sonic cannon before he and Victoria flee the ship. The Doctor revives the Base staff, who were rendered unconscious by the sonic blast, and works with Penley to recalibrate the Ioniser. The computer gives a fifty-fifty chance that the Ionizer will explode when trained on a spacecraft with an ion engine; Penley tells Clent to work without the advice of the computer. When the computer overloads, Penley takes charge and starts the Ioniser.
The Martian craft begins to power up, but does not get far before it is destroyed by the Ioniser. The ship explodes without starting a chain reaction, which solves both the problem of the Ice Warriors and the glacier. Their work done, the TARDIS crew slip away as some green shoots emerge through the melting snow.