UNIT officers Geoff Paynter and Mark Barrington follow Ukranian courier Serji Bulyjin to Los Angeles, where Bulyjin is arranging the illegal sale of plutonium to Paolo Sanger, head of the international communications conglomerate InterCom. When Bulyjin delivers the plutonium to Stephen Joyce, the president of InterCom's R&D division, Joyce repays him by turning him over to InterCom's scientists for use in their genetic experiments. However, the scientist Chung Sen's researches have hit a dead end, and it appears that they can progress no further without access to an extra-terrestrial. Worse, Chung Sen's trusted assistant Kyra O'Shaughnessy has betrayed him and stolen a CD-ROM containing the entire invasion plan. News of the theft reaches the CIA, and Brigadier Lethbridge-Stewart's old nemesis Control -- who decides to help InterCom to get hold of an alien.

The Doctor is summoned to London in the year 1999, where his old friend Lethbridge-Stewart has an assignment for him. UNIT operatives have been unable to determine the true nature of Paolo Sanger, who has recently purchased a disturbing amount of black market plutonium. Fearing that InterCom may be a front for an alien invasion, the Brigadier asks the Doctor to act as an agent provocateur and find out what's really going on. The Doctor thus takes Tegan and Turlough to L.A., where they find the city under threat from the Sons of Nostradamus, a group of violent anarchists who are bombing public sites while awaiting the arrival of the man who will guide them safely through the end of days. The bombings are causing InterCom no end of headaches, but what Sanger doesn't know is that his own security chief, Shawn Ryman, is in fact in league with the Sons' leader Jon Newton. Meanwhile, as the Doctor plans his strategy Turlough goes out for a night on the town -- which is a mistake, as Control has learned of the Doctor's arrival and has alerted InterCom. Turlough allows a stunning blonde named Eva to pick him up in a bar and take him home -- where she drugs him, questions him about his involvement with UNIT, and turns him over to her fellow aliens for genetic analysis.

The Doctor reports Turlough's disappearance to the Brigadier, who flies out to L.A. to take charge of the investigation. The Doctor and Tegan, meanwhile, visit InterCom in the guise of a Cambridge professor and his assistant, and are given a tour of the laboratories by Joyce and Dr Richard Lewis. The Doctor provokes the insecure Lewis into letting slip what he had already suspected; most of the scientific advances supposedly made by InterCom are in fact derived from alien technology. Meanwhile, Paynter and Barrington join a public tour of InterCom, but slip away at the first opportunity -- and find human scientists working on an alien spacecraft in the restricted areas. They are spotted by security guards, but although Ryman sends his deputy to kill them, the Sons of Nostradamus set off a bomb in InterCom's courtyard and in the confusion Paynter and Barrington escape without ever realising they had been targeted. Back at UNIT HQ, they share their story with the Doctor and Tegan. InterCom is definitely a front for an extra-terrestrial operation -- but who are the aliens and what is their agenda?

The stolen CD-ROM makes its way through a string of couriers and finally reaches Control. The data confirms his suspicions; soon Earth will become a battleground between two warring alien species, and could be destroyed in the process. All Control can do now is wait and try to guide events towards the best outcome. Meanwhile, Lewis finishes probing and analysing Turlough, and confirms that he is indeed alien. Ryman then shoots Lewis for his slip-up during the Doctor's visit, and orders Eva to prepare Turlough for questioning; before they extract his DNA, they must determine just how much UNIT knows about their plans.

Having struck a blow against InterCom, the Sons of Nostradamus plant a bomb at UNIT, killing Mark Barrington. The Doctor blames himself for letting things go too far, and reluctantly asks the Brigadier to arrange a meeting with the CIA; he's suspected for a long time who's really in charge there, and it's time to pool information. He and Control eventually come to a tentative agreement, and with Control's information the Doctor is able to identify the aliens. They are the Jex, a savage warrior species struggling to maintain their falling empire -- and with the foothold they already have through InterCom they could subjugate the human race within months. Sanger's black market plutonium will be detonated in the atmosphere, altering Earth's climate into one more suitable for the Jex; Turlough has been kidnapped so they can study his DNA and use it to create human hybrids, who will be able to survive on the new Earth to serve as the Jex's slaves. As if this weren't bad enough, the Jex are always followed by the Canavitchi, their mortal enemies. They are a former slave race who rebelled and launched a war which nearly brought down the Jex empire, and they were brutal enough even before the Jex invasion got them organised. Rather than save humanity from the Jex, they're more likely to destroy the Earth in order to wipe out all trace of their enemies...

Tegan is worried about Turlough, and Sergeant Dave Milligan offers to take her out on the town to relax. Pop star Johnny Chester is signing copies of his first novel at a nearby store, and although Milligan picks up an autographed CD, Tegan isn't interested in meeting a pop icon -- and thus misses the chance to meet someone who will have an important influence on her future. Meanwhile, Paynter is given compassionate leave to come to terms with his partner's death, and at the Doctor's suggestion, Milligan takes him and Tegan to Las Vegas for some R&R. However, while driving through the desert they are buzzed by a UFO and their car battery dies. They are forced to walk to the nearest gas station, but the attendant is an assassin set down by the UFO, and he kills Milligan before Paynter can shoot him. As the attendant dies he reveals that there are two more assassins on the way, and Paynter and Tegan flee to a nearby shack, hoping to lure the assassins into a trap. Paynter shoots the first assassin, and although the second shoots Paynter in the leg, Tegan distracts him long enough for Paynter to kill him as well. Paynter and Tegan return to the gas station and call UNIT for a pickup; they have been drawn closer by their shared experience, but their relationship remains abrasive.

Kyra is recaptured and tortured, and when she dies under interrogation the Jex find that she wasn't human. When Sanger learns that a Canavitchi ship has been spotted over the Nevada desert this confirms that the Jex's enemies have tracked them to Earth, but Sanger remains unaware that his own security chief is a Canavitchi agent. Ryman has convinced Jon Newton that he is the alien messiah who will save the Sons of Nostradamus, and is using them to harass InterCom and delay the Jex invasion until his people are ready. Ryman manipulates Newton into sacrificing his life to bomb InterCom's head office, and then visits Control, who hands over the CD-ROM. Satisfied, Ryman calls in his brethren to attack. Control, by now, has realised that the game has gone too far; the Canavitchi are even more brutal and savage than the Jex, and they do not fear death. When UNIT comes to Control for help he'll be all too ready to give it to them.

As Turlough recovers from his brutalisation, he overhears Eva discussing the invasion with her comrades. He has heard of the Jex, and is able to put together the pieces and deduce what they need him for. When Eva returns for him, he strangles her and beats her to death with his own manacles in a single terrified and enraged burst of strength, and staggers out of her apartment into the streets, where he is picked up by the LAPD and returned to UNIT HQ.

The Doctor and the Brigadier visit InterCom to confront Sanger and his fellow Jex, and when the Doctor tries to provoke Sanger into slipping up by pointedly mentioning the Canavitchi, he realises from Ryman's reaction that Ryman is a Canavitchi agent. The furious Jex turn on the traitor and tear him apart, and the Doctor and the Brigadier retreat, the Brigadier throwing a grenade back into the boardroom as he goes and thus wiping out the invasion spearhead. UNIT forces then storm InterCom, taking out the Jex and capturing their human collaborators, but the Doctor knows that they've acted too late; the Jex fleet is on its way, and the Canavitchi will be waiting for them, turning Earth into a war zone with humanity caught in the middle.

Control finally tires of waiting for UNIT to contact him and contacts them instead, offering to put all of the CIA's resources at their disposal -- as it was largely due to the CIA's attempt to manipulate both the Jex and the Canavitchi that things have gotten this bad. With the help of CIA liaison Dwayne Landmott, Paynter locates and arrests the leaderless Sons of Nostradamus, and manages not to kill the man who killed his partner. Meanwhile, with Landmott's help, the Doctor converts the Earth's satellite communication network -- including many of the satellites sent into orbit by InterCom -- into a force field generator which will shield the Earth from the worst of the combat to come. As the two fleets arrive and battle is joined, all humanity can do is sit behind their shield and wait it out. Fortunately, the field holds, and eventually both alien armies batter each other into submission and retreat, too busy tending their wounds to bother with the Earth.

Humanity has survived, but more by luck than anything else. Tegan bids farewell to Paynter, both knowing that their relationship can't last. The Doctor advises the Brigadier to enlist the CIA's help to track down any remaining Jex or Canavitchi agents. Control is satisfied with the outcome; there will be many more games to play in the coming millennium, and with the Doctor on their side, how can they lose?