A group of hippies attending the Redborough '70 rock concert on Viscount Rose's estate see strange lights in the night sky, and soon afterwards, people are found dead in the surrounding area, as if torn apart by wild animals. The Doctor is called in when a radar array which he had specially modified picks up something entering the Earth's atmosphere, but while on their way to the array, he and Benton are attacked by masked commandos who attempt to kidnap the Doctor. The Doctor manages to drive them off, and he and Benton continue on to the array, where they confirm that an alien mass did indeed enter the Earth's atmosphere. The Doctor draws a connection to the Redborough '70 sighting, and tries to enlist the help of Viscount Rose to investigate; however, Rose is an aging hippie who refuses to help an agent of the Establishment. Before the Doctor can press his case he is attacked once again, and this time his captors identify themselves as agents of the Soviet Union. He manages to escape, and the Brigadier -- whose hands are full with the arrival of American agent Bruce Davis, and security measures for Professor Bernard Trainor's press conference on recent unmanned Neptune probes -- orders Benton and Yates to remain with the Doctor at all times.

Since Trainor's conference is to take place at Cambridge, Liz Shaw is acting as UNIT's liaison. She invites the Doctor to a party thrown by an old friend, where a beautiful blond woman takes Yates into the bedroom and knocks him out while her soldiers kidnap the Doctor once more. This time the Brigadier is prepared, but unfortunately one of the Soviets is shot by a trigger-happy UNIT soldier while surrendering. Worse, the Brigadier recognises the blonde as Captain Valentine Shuskin -- an agent of the Soviet branch of UNIT. By assaulting a UNIT operative from a foreign country on his native soil, Captain Shuskin may have started a war and caused the end of UNIT. Shuskin insists that her country is in desperate need of the Doctor's help, and that the Brigadier himself had refused to grant permission. She provides as proof official forms which were apparently signed by the Brigadier himself -- forms which the Brigadier has never seen in his life. The Brigadier permits the Doctor and Liz to depart with Shuskin, and leaves Yates in charge while he goes to Geneva to investigate what could be a conspiracy at the very heart of UNIT.

Red Army divisions have gone missing in the Siberian forest while investigating the break-up of an alien mass in the atmosphere, and the only evidence to come out of the area are photographs of a mercury stream leading to alien mine workings. Shuskin accompanies the Doctor and Liz to the forest to investigate, but their escort is attacked by bat-like humanoids in flight harnesses. The aliens are too numerous and agile for the Soviet helicopters to destroy, but the Doctor jury-rigs a force field by using his sonic screwdriver to conduct the helicopter's electrics directly into the hull, enabling them to land safely. On the ground, they find the remains of the previous expeditions, and are attacked once again by the hostile, goblin-like aliens. The Soviets manage to capture one of the aliens, and the Doctor performs the dangerous telepathic "soul-catching" rite to determin its purpose in coming to Earth. He learns that these are the Waro, the inhabitants of Neptune's moon Triton, and that they have come to the Earth to mine cobalt. The Waro are possessed of an overwhelming hatred of all other life, and when the captive Waro senses the Doctor's presence within its mind, it kills itself, sending the Doctor into a coma.

UNIT's new American liaison, "Bruce Davis", is in fact Thomas Bruce -- a CIA agent with orders to copy UNIT's secure files and cause as much collateral damage as he can before departing. Unaware that there is an enemy agent in their midst, Yates and Benton continue to investigate the Redborough sighting, but get nowhere with the hostile flower children. Only Arlo, leader of the so-called Venus People, tells them that soon God will return from Venus to save the chosen and unleash Armageddon upon the rest. Benton finds Arlo oddly familiar, and soon after returning to UNIT he recalls seeing a news photograph of Arlo standing next to Viscount Rose; however, Bruce has planted a bomb in the Doctor's laboratory, and before Benton can tell anyone what he has remembered, he is caught on the outskirts of the explosion and knocked out. Meanwhile, Bruce downloads UNIT's secure files, and then murders a technician, disfigures the body with hydrochloric acid and disguises him in Bruce's own clothes. He then departs, mission complete, leaving the UNIT staff under the mistaken impression that it was the technician who murdered Bruce. By the time they realise their mistake, Bruce has evaded the roadblocks set up to stop the wrong man, and has made his way to the coast, where a hovercraft is waiting to collect him.

In Geneva, the Brigadier contacts his superior, Major-General Hayes -- who significantly doesn't dismiss the Brigadier's claims out of hand. Yates contacts the Brigadier following the explosion in the Doctor's lab, and reports having found a UNIT serial ID number amongst the remains of a Russian bomb. The Brigadier, sure that this is a crude attempt to frame the Soviets, breaks into UNIT's secure file room to trace the bomb's ID code, but is caught doing so. Rather than discipline him, however, Hayes confirms that there is a traitor within UNIT -- Major Mick Houghton -- and orders the Brigadier to dispose of him quietly. The Brigadier traces Houghton to an abandoned warehouse in Geneva's red-light district, but instead of killing Houghton, he contacts him and asks for an explanation. Houghton has in fact been investigating the same conspiracy, and it appears that Hayes is involved and is trying to dispose of two irritants at once. The Brigadier and Houghton try to escape with Houghton's collection of evidence, but Hayes sends compromised troops and the Swiss police after them and Houghton is shot trying to fight his way free. The Brigadier is captured and taken to an airfield where Thomas Bruce is waiting to turn him over to his own boss, Control. Control's organisation has been dealing with aliens since the 1940s, and now the new kid on the block is going to meet Earth's real anti-alien taskforce.

The Doctor recovers just in time to stop Captain Shuskin from calling in a nuclear strike, telling her to wait until they learn more about the Waro. Now knowing them to have fragile bodies that rely on their artificial harnesses for strength and agility, he attempts to generate a radio signal which will jam their equipment. He is attacked before he can finish, but Liz completes his work and drives the Waro away. While the Doctor recovers, Shuskin and Liz continue on ahead to the mine workings, which they discover to be false. They return to the helicopters and depart, now knowing the Waro incursion in Siberia to be a decoy, intended to divert attention from the real invasion taking place somewhere else.

Shuskin accompanies the others to England, where Liz, wondering if the Waro may have been attracted to Earth by the recent Neptune probes, attempts to speak with Trainor -- only to be run off the road by a limo belonging to Viscount Rose. Meanwhile, Benton, suffering from concussion, checks himself out of the hospital and tries to infiltrate the Venus People. Aware that he is not one of them, they slip him a tab of acid, and while he goes on a very bad trip, the Waro arrive and slaughter the rest of the Venus People. Arlo escapes and rushes to Rose's estate to accuse him of betraying them, only to be killed by the waiting Waro. Benton is taken back to UNIT's sickbay, while the Doctor investigates the Redborough sighting and finds the remains of a Waro craft's propulsion unit in the sea. The Waro have removed all of the parts necessary to construct a cobalt bomb, and require only a fissile isotope of cobalt which cannot be found on Triton. Yates arranges for the UK's supplies of cobalt to be moved to safety, but the convoy is strafed by UFOs which destroy the entire consignment. Only the Doctor's modified radar array is able to detect the UFOs, and it traces their flight path back to the USA. The UFOs are in fact American craft, reverse-engineered from alien technology, and when Yates learns that the Americans recently moved a large consignment of cobalt-60, the Doctor realises that the Americans are setting their own trap for the Waro, and destroyed the British supplies of cobalt-60 so that the Waro would not be distracted from the Americans' bait.

The Brigadier is a prisoner in Area 51, a bunker where the alien Nedenah have been held captive by the American army ever since the Roswell crash. CIA scientists have studied their technology for decades, and are ready to lure the Waro into a trap, destroy them, save the world and discredit the upstart UNIT. They have, however, seriously underestimated the Brigadier, who manages to escape from his guards and tries to make contact with the Nedenah. Rose and Trainor are also trying to do so; Trainor's Neptune probes have put him in contact with a race of aliens thanks to Rose's funding, and Trainor believes that they are here to rescue the benevolent Nedenah from their captors. He learns almost too late that Rose has in fact been in contact with the Waro, the Nedenah's ancient enemies, who have ordered him to kill them. Rose believes that humanity is hopelessly corrupt, and intends to help the Waro wipe out the human race so the Earth can start over again. The Brigadier overpowers Rose, and leaves him in the Nedenah cells while he, Trainor and the Nedenah retreat to the Nedenah's saucer -- which the CIA have never been able to break into. Rose is found and shot by Control.

The Doctor, Liz, Yates and Shuskin arrive at Area 51 moments before the Waro launch their attack. The Americans have seriously underestimated the Waro's numbers and ferocity, however, and despite the use of reverse-engineered Nedenah fighters, the Waro destroy their opponents and overrun the base, seeking its cobalt-60. The Nedenah attempt to escape, but their ship is brought down by the Waro; however, it will soon repair itself, and the Nedenah manage to recover a chemical weapon which will remove the blocks the Waro have placed in their brains to channel their agression against anything that is not Waro. The Doctor's jamming device enables them to reach a jet fighter, which they use to disperse the chemical agent over the base, but before the agent can get to work the Waro bring down the plane. Trainor dies in the crash, but the chemical agent then does its work, causing the entire Waro invasion force to slaughter themselves.

The Nedenah depart, their work done, while Shuskin returns to the Soviet Union and the others return to England. Yates admits to himself that he was overwhelmed by the pressure of command and vows to do better next time. The Doctor, however, suspects that the CIA is being supported by another, more familiar Agency, and fears that UNIT's troubles are not over. Back in America, Bruce finds proof in the files which he stole from UNIT that his son's leukemia was caused by his ex-wife's exposure to Nedenah technology; but despite this personal betrayal, he will never be allowed to leave the CIA.