Captain Andrea Winnington is keeping an eye on the comings and goings at UNIT HQ, but fails to recognise Sir Alistair when he enters the building with Chaudhry. Once inside, Sir Alistair scans the building for bugs and wiretaps, and adds a device to the phone lines that will enable him to scan every call going through the British telephone system. Chaudhry goes through her paperwork and discovers that UNIT has been assigned to investigate a mysterious flu outbreak that began a few weeks ago; government scientists have been unable to identify its origin, and its victims are growing aggressive and violent as their condition worsens and their flesh literally begins to rot on their bodies. 600,000 people have been infected in Britain alone, and the world is beginning to panic as cases are reported in other countries. Sir Alistair thus contacts his old friend, Harry Sullivan, who is currently doing secret research for NATO, and asks him to analyse a tissue sample from one of the disease’s victims. In the meantime, he advises Chaudhry to get some rest for her troops’ sake, and joins a patrol to see what the situation is like out on the streets. Winnington spots the patrol leaving UNIT, and calls her superiors at ICIS, telling them that they have a perfect opportunity to set the next stage of their plan in motion...
Meanwhile, Francis Currie and his cameraman, George, are out on the streets, reporting on the outbreak. The police have called to St Catherine’s hospital, one of the first to be put aside exclusively for victims of the new disease -- and as Currie reports from outside, a mob of patients bursts out of the hospital, screaming and raving as the flesh rots on their bodies. One of the patients, maddened with pain, actually bites George on the arm before he and Currie can get away. As Currie and George shelter nearby, Currie spots an army Jeep pursuing one of the escaped patients into a nearby alley, and when he and George investigate, they see soldiers gun down the escaped patient without a word of warning. The soldiers leave, apparently without realising that they’ve been caught on camera -- and when George rewinds the tape, Currie recognises the insignia on the soldiers’ uniforms as that of UNIT.
When Sir Alistair returns from patrol, Chaudhry reports that they’ve picked up one of Winnington’s phone reports, which made it clear that she’s hiding nearby and spying on them -- and in the course of the conversation, Winnington inquired after Brimmicombe-Wood’s health. Chaudhry traced the call to a disused army base in Markham, which is presumably where Brimmicombe-Wood is being held. Sullivan then contacts Sir Alistair and sends him a secure e-mail indicating that the “flu” virus is alien and artificial in origin; it is rewriting its victims’ DNA, driving them mad with pain in the process. Sullivan and his people are working on a cure, but the situation is rapidly getting worse; the PM has been forced to call in the army to maintain order, and although he insists that he is not declaring martial law, his announcement is greeted with derision and anger.
Corporal McLeish catches Francis Currie trying to break into UNIT HQ through the back, but Currie explains that he’s just trying to get to Chaudhry without being spotted by anyone who might have UNIT under surveillance -- which is just as well, since Winnington still has them under observation. Currie is here to show Chaudhry the tape of the so-called UNIT patrol gunning down an escaped patient in cold blood; by now, he’s familiar enough with UNIT to recognise that the soldiers weren’t using standard UNIT uniforms or weapons, and he trusts Chaudhry enough to know she wouldn’t authorise something like this. Sir Alistair realises that Winnington was waiting for a patrol to go out so she could set this operation in motion, and when McLeish scans the radio frequencies that ICIS is known to use, they discover that troops are already on their way to UNIT HQ, ready to act once the tape has been made public. Currie had already worked out that he was allowed to tape the murder so ICIS could use him to discredit UNIT, but he now admits that he ran off a copy and left the original with George just in case he was wrong. Even as they speak, ICIS troops are beating George up and taking the tape.
Chaudhry and Sir Alistair show Currie’s tape to their troops and ask them to make a decision. They have been ordered to stay where they are and wait for reinforcements, but they now know that the “reinforcements” will be ICIS troops sent to arrest them for a crime they haven’t committed -- and it’s unlikely that many of the UNIT troops will survive being arrested by ICIS. Nevertheless, Chaudhry and Sir Alistair leave it up to each soldier’s individual conscience to decide whether they wish to disobey orders and go on the run; happily, the soldiers all decide to throw in their lot with UNIT. As they prepare to move out, Sir Alistair tells Chaudhry to drop the formalities and just call him “Brigadier.” The Brigadier thus leaves UNIT HQ by the front door, with Sergeant Willis as his driver, and this time, Winnington recognises him and sets off in pursuit. As soon as she’s gone, Chaudhry and her troops move out -- accompanied by Currie, who insists upon sticking with this story to the end.
The Brigadier and Sergeant Willis lure Winnington away from UNIT HQ and then fake a car crash, leaving Winnington convinced that they’ve both gone up in flames. Winnington wonders if the Brigadier considered his cause worth dying for, as she no longer believes that her own is worth it. Once Winnington has left the scene, the Brigadier and Willis set off to join forces with Chaudhry. On the way, they see packs of raving plague victims swarming through the streets, attacking innocent bystanders and literally eating them alive. However, Sullivan has some good news when the Brigadier contacts him: some new friends have offered their help in analysing the virus and finding a cure...
Currie insists upon accompanying Chaudhry and her team into the army base in Markham, but Chaudhry refuses to give him a gun. The base seems to be all but unguarded; the UNIT troops encounter only one ICIS soldier, whom they overpower. Currie offers to hide the unconscious guard while the others search for Brimmicombe-Wood -- but once he’s alone, he pockets the guard’s gun. Meanwhile, Chaudhry locates the base’s interrogation cells, and, to her delight, finds Brimmicombe-Wood alive and well inside one of them. He is amazed to see her, and she’s relieved to have him back in charge. She gives him a gun and updates him on the situation outside, including Sullivan’s work on the virus; however, he tells her that his captors have let slip much of what’s been happening in his absence, including Will Hoffman’s death. Before leaving, he insists upon having a look around the enemy base while they still have a chance.
Deep in the base, ICIS has stored the alien spaceship that they stole from UNIT, and Chaudhry finds evidence that scientists employed by ICIS have been examining it -- and in so doing, they released the mysterious virus that is sweeping the globe. Brimmicombe-Wood, surprised to learn that Sullivan’s group at Deepcastle have already identified the virus as alien, confirms that the scientists who analysed the virus after it infected the research staff have determined that it’s a food additive designed to make human flesh a more palatable meal for the alien race that designed it. This particular ship crashed, and the aliens never arrived on Earth to follow up with a harvest, making the plague even more tragically pointless than it already is. But Chaudhry is more interested in learning just how Brimmicombe-Wood found all of this out, as she can’t believe that his captors were quite so careless with their secrets... and she’s noticed that he somehow knew where Sullivan’s team was working even though she never mentioned Deepcastle in front of him. Just as she’s putting the pieces together, Brimmicombe-Wood strikes her down and pulls a gun, reminding her that his “cell” wasn’t under guard. He isn’t a prisoner of ICIS, and never has been; he’s its commanding officer.
Brimmicombe-Wood holds Chaudhry at gunpoint and forces the UNIT troops to drop their weapons, revealing that he’s been in charge of ICIS since the very beginning. All the time he was supposedly UNIT’s CO, he was spying on them and setting them up for a fall. He claims that he’s doing this because he’s a loyal soldier who swore an oath to protect the country -- against the people who are turning his country’s sovereignty over to foreign countries, some of whom have been at war with Britain within living memory. He’s seen his own men killed fighting to protect other countries that didn’t want them there, and like the rest of ICIS, he’s decided that it’s time to put Britain’s interests first. Sickened, Chaudhry realises that Brimmicombe-Wood is responsible for everything that’s happened to UNIT in recent months, including the deaths of people who respected him -- but he mocks her despair, cruelly asking if it’s true that she had a crush on him.
Fortunately, Currie has overheard all of this from hiding, and he now emerges, pointing his gun at Brimmicombe-Wood. Realising that the other troops will have a chance to pick up their guns before he can shoot both Chaudhry and Currie, Brimmicombe-Wood chooses to retreat, locking himself in the spaceship’s control room and calling for reinforcements. The UNIT forces flee, but are forced to fight their way past the ICIS troops now rushing into the base; Chaudhry is reluctant to order her troops to fire on British soldiers, but has little choice. The UNIT forces use stun grenades and smoke to cover their escape, and get out with few casualties -- but Chaudhry doesn’t have any further plan, as she was expecting Brimmicombe-Wood to be in charge at this point. Worse, she’s just revealed to the enemy how much NATO knows about the virus, and what they intend to do about it.
Brimmicombe-Wood and his troops pursue the UNIT forces to a nearby airfield, where the Brigadier and Willis are helping NATO forces to load a lorry aboard a Hercules transport plane. Once the UNIT forces are aboard, the Hercules takes off; Brimmicombe-Wood orders his troops to shoot it down, but they fail to do so, and the NATO forces retreat while ICIS’ attention is divided. Furious, Brimmicombe-Wood retreats to HQ to plan his next move, unaware that Francis Currie is hiding in a nearby storm drain. Once the ICIS troops have gone, he emerges and makes his way back to London. A warrant has been issued for his arrest and the Planet 3 offices are surrounded by ICIS troops; however, he knows a number of secret ways into the building, and he manages to get in, contact the badly beaten George, and convince him that together, they can get back at the people who did this to him.
Chaudhry is devastated by Brimmicombe-Wood’s betrayal, but despite her personal feelings, she must put on a brave front for the troops who are looking to her to lead them into battle. The Brigadier reveals that the Silurians have helped Sullivan and his colleagues at NATO to develop an antidote to the virus; however, while it will prevent anyone else from falling ill, those who have already had their DNA rewritten by the disease may be beyond help. UNIT HQ in Geneva have arranged for the antidote to be launched into the Earth’s atmosphere via an old missile facility in the former Soviet Union -- but they’ll have to get there first, and ICIS has scrambled RAF planes to pursue the Hercules and shoot it down. The Hercules manages to reach international airspace, where a UN escort is waiting -- and when the RAF planes fire a missile at the Hercules, one of the UN’s pilots swoops in and takes the hit. The remaining RAF fighters are forced to retreat under fire, and the Hercules reaches its destination.
Unfortunately, it’s a half-hour drive from the airstrip to the launch site, and when Chaudhry and her troops arrive, they find that Brimmicombe-Wood and the ICIS troops have beaten them to their destination and seized control of the facility. The Russian rocket scientists are gunned down before the UNIT forces’ eyes, leaving the Brigadier with no choice but to install the missile payload himself while Chaudhry and her troops hold off ICIS. The Brigadier and Willis manage to get their payload to the rocket, and, with the help of the surviving Russian ground crew, they get the antidote installed on the missile’s warhead. Before they can launch the missile, however, Winnington arrives and shoots Willis, wounding her. Winnington threatens to destroy the launch controls unless the Brigadier stops her, but he realises that she’s deliberately trying to provoke him into killing her. When he presses her, she breaks down and admits that she no longer believes in the cause she’s fought for her whole life; she’s been betrayed by ICIS and her own father, while UNIT sticks together and protects their own. But while she no longer knows what she believes in, she’s determined not to fail in her duty again. Before she can destroy the controls, however, the Brigadier shoots her -- in the hand, injuring but not killing her. The Russian troops restrain the despairing Winnington, placing her under arrest, while the Brigadier programmes the missile to launch and destroys the controls so it can’t be stopped.
Brimmicombe-Wood and his troops try to flank the UNIT troops under cover of smoke grenades, but Chaudhry realises what they’re doing and leads her own forces around the back of the building into battle. As the UNIT and ICIS troops engage in hand-to-hand combat, Brimmicombe-Wood and Chaudhry engage in a very personal fight. Brimmicombe-Wood is physically fitter than Chaudhry, who’s still recuperating from her weeks-long coma -- but just as it seems that he’s won the fight, Chaudhry shows him that she’s holding the pin from a grenade. Brimmicombe-Wood instinctively turns to look behind him, and the flash grenade goes off, blinding him. Chaudhry beats him until he’s down, and then keeps beating him until the Brigadier arrives to stop her. The missile goes up, releasing the antidote, and Chaudhry places Brimmicombe-Wood under arrest on charges of terrorism, treason, and anything else she can think of. Brimmicombe-Wood insists that he was doing his duty for Britain and that it’s the Brigadier and Chaudhry who are the traitors -- and the terrible thing is, he really believes it. The Brigadier reminds Brimmicombe-Wood that he joined the army to defend the lives of the innocent, and has him and his men taken away under arrest -- and once they’ve gone, Chaudhry succumbs to her fresh injures and collapses.
Much later, Chaudhry is back in Britain, once again recovering from her injuries in hospital. Currie and George have broadcast the footage that Currie surreptitiously recorded during UNIT’s raid on ICIS HQ, and as a result, ICIS has been shut down, its leaders are facing charges of treason, and UNIT has been cleared of all charges and given new funding. The Brigadier visits Chaudhry in hospital and reveals that she’s been appointed as UNIT’s new CO; however, she realises that she’s going to need some unofficial help and advice to make a go of it, and since UNIT’s previous scientific advisor is unavailable, she offers the position to the Brigadier. Amused, he accepts the job.