3 March 2068: Captain Karl Taylor is sent to investigate mysterious alien signals from the Moon, but the sights and sounds of the alien “city” he encounters are entirely incomprehensible to human perceptions. Taylor thus orders his people to open fire, apparently fearing that they are under attack. This is the start of a war between the alien Myloki and PRISM, the secret organisation created to fight the invaders. The Myloki attack by transforming ordinary human beings into their puppets; most are merely drone-like zombies known as Shiners, but two are different. One is Captain Taylor, who is sent back to Earth as a walking, indestructible, reanimated corpse, an emotionless killing machine. The other is Captain Grant Matthews, who is killed and duplicated while on a routine escort mission; however, his duplicate is caught and deprogrammed of his Myloki conditioning, and, like Taylor, is found to be literally indestructible.
Eventually, it is discovered that the Shiners are being controlled via signals from the Myloki “base” on the moon; later theories will suggest that this is an area where the barrier between the human and Myloki realities is weak, and that Taylor’s expedition may be the very thing that allowed the Myloki to gain a foothold in this reality. Matthews is sent to the base with a 20-megaton bomb strapped to his body; once he detonates it, all of the Shiners in the world drop as though their connection has been severed, and even Taylor -- who had been lured into a trap by Matthews and sealed in 6,000 litres of modified liquid concrete -- stops showing life signs. However, the war effort has drained so much of Earth’s resources that the world economy collapses, and the planet falls into chaos and social disorder. A disgruntled member of PRISM, Neville Verdana, then publishes a tell-all exposé revealing the truth about the war -- and revealing that Taylor survived the nuclear explosion and is still alive somewhere on Earth. In the face of public outrage, PRISM is forced to go underground as a clandestine organisation named SILOET, but continues to draw on the shattered world’s resources to maintain a constant watch in case the Myloki should return...
2098 AD: SILOET has abandoned its showy sky headquarters, the floating base called SKYHOME, for more prosaic quarters behind the front of the British Film and Television Corporation. Commander Hal Bishop, who was forced to kill his own wife during the war when she became a Shiner, is called away from his holiday when intruders (the Doctor, Jamie and Zoe, as it later turns out) are detected on SKYHOME. Bishop’s second-in-command, Alex Storm, has SKYHOME flooded with nerve gas and sends a collection team to capture the intruders. The intruders recover on the way back, overpower the collection team and try to flee from the BFTC building -- but while the young man and woman escape, the older man is shot in the head. Bishop has the body sent to Dr Koslovski for an autopsy, but Koslovski discovers that, despite the apparently fatal brain damage, the man’s body is repairing itself, as if the man’s DNA is being rewritten from the ground up. Koslovski manages to stabilise the patient’s condition using genetic material extracted from Shiners, but it seems that the man is indestructible -- which would suggest that the Myloki have returned...
Six months later, the patient begins to show EEG readings matching the signals known to link the Myloki to the Shiners. He then awakens from his coma, demands a mirror, and seems surprised to find that his appearance hasn’t changed; apparently the genetic material that was put into his body inhibited some sort of natural process. He refuses to answer any questions until his friends, Jamie and Zoe, are returned to him, and Bishop, still convinced that the patient heralds a new Myloki invasion, sends his men out to find and retrieve the other two fugitives. Privately, he informs Professor Graham that they may have a subject for his experiments. However, Storm has a different theory; he believes that the patient is linked to old UN reports of a mysterious figure who frequently saved the Earth from alien invasions and was capable of changing his appearance when grievously injured...
Jamie has joined the City Militia, a ragtag army that polices the ghettos of West London. Injured in his escape from SILOET, separated from Zoe at a city hospital, and delirious from shock after seeing SILOET troops shoot and kill the Doctor before his eyes, Jamie has fallen under the spell of the charismatic Mr Mackenzie, the Scottish leader of the City Militia. Jamie has had to do terrible things to survive in the harsh environment of the city, and the only thing that keeps him going now is his desire to avenge the Doctor’s death. Mackenzie eventually decides that Jamie can be trusted, and takes him to a sealed chamber beneath Kensington Town Hall, where he has been keeping the zombie-like Shiners penned in cages. Desperate to find a reason for the fall of civilisation, Mackenzie has come to believe that the Myloki are agents of God sent to punish mankind for its hubris, and the traumatised and somewhat deranged Jamie accepts this as true.
Satisfied, Mackenzie sends Jamie on a mission to raid the West Home Flats retirement community, to investigate reports that there’s a Shiner locked up in the cellar. It turns out that a youth gang has been using the cellar as their home, and when the Militia bursts in, the frightened gang members open fire, killing Jamie’s sergeant. Jamie beats one of the young gang members nearly to death in a fit of rage, and when he finds that the gang was keeping a Shiner chained up as a mascot and feeding it cats to keep it pacified, he disobeys orders and shoots the Shiner dead. As the militia prepare to move out, a squad of MOVERs -- old PRISM vehicles -- drive up to the area and deploy gas weapons when the militiamen open fire on them. Just as the enraged Jamie is about to charge the MOVERs, however, one of his fellow militiamen, Gregor, tackles him and injects him with a knockout drug. Gregor has been a secret SILOET agent all along, and now Jamie is back in their clutches.
Shortly after getting Jamie to the hospital, Zoe was kidnapped by scouts from the City Republic, a walled community owned by what remains of the world banks after the collapse of the financial markets. The Republic is a caste-driven society in need of slave labour; though the slaves are denied luxuries, they are given enough food and shelter to meet their needs, and are slowly but surely building a workable community. Believing the Doctor to be dead, Zoe tries to lose herself in the logic of her new situation, and eventually her excellent work is noted and rewarded with a promotion. Her new supervisor, executive officer Mark Khan, falls in love with her and asks her to marry him; his kindness awakens Zoe’s softer side, and she accepts his proposal. However, Mark and Zoe are then lured into a trap set by Alex Storm, who shoots and kills Mark without a moment’s hesitation and takes the devastated Zoe back to SILOET.
Once Bishop informs his mysterious patient that his friends have been recovered, the patient identifies himself as the Doctor. He is allowed to see his friends, but they have both been deeply traumatised by their experiences. Zoe has tried to commit suicide and is now under sedation in the medical wing, but once she sees that the Doctor is alive, she is able to let out her pent-up emotions and start down the road to recovery. Jamie, however, has had to do terrible things to survive in the world outside, things he could only have done if the Doctor was dead; he can’t afford to let himself believe that the Doctor has been alive all along, and he therefore insists that the Doctor is really a robot duplicate and vows to kill this “duplicate” once he gets the chance.
Bishop is called before SILOET’s command council to justify his actions, which have compromised SILOET’s long-term strategies to keep the Militia and the Republic under control. When the Doctor is brought before the high command for questioning, his genial, bumbling attitude does little to support Bishop’s claim that he’s a Myloki agent -- but just as the commanders are about to pass judgement, the Doctor reveals that Bishop is partly correct. When Koslovski injected the Doctor with genetic material from the Shiners, it not only inhibited his natural regenerative process, it momentarily put the Doctor in touch with the Myloki -- and although the Doctor’s body has now rejected the alien material, he knows that the Myloki are returning.
Contact is lost with SILOET’s early warning system, SEWARD, and fireballs streak down out of the sky, striking areas that contain remnants of the earlier invasion. One of the fireballs strikes Kensington Town Hall, where Mackenzie is praying before his captive Shiners, unaware of the true nature of the buried impulse that drove him to bring them all together into one central location. Despite the Doctor’s objections, Bishop and Koslovski sedate Jamie and take him to the remains of the Town Hall to get his impression of what’s happened there. To Jamie’s horror, the alien energy seems to have transformed the entire landscape into a rotting, diseased alien parody of itself. In Mackenzie’s inner sanctum, Jamie sees a shapeless humanoid mass shifting in a chair, and he grabs the terrified Koslovski’s pistol and empties it into the figure. He is then taken back to SILOET, but refuses to believe what he’s seen, instead telling himself that SILOET is trying to trick him into doubting his own convictions so that he will betray the real Mackenzie.
After researching the previous war, the Doctor concludes that the Myloki are from somewhere far stranger and more alien than mere outer space. He also concludes that the half-human, half-Myloki Grant Matthews is the key to the Myloki’s return -- and Neville Verdana, whom the Doctor believes had an ulterior motive for writing the exposé that brought down PRISM, may be the only one who can help them find Matthews. Bishop sends Storm to help the Doctor track down Matthews, but before they leave, Bishop gives Storm a mysterious device constructed by Professor Graham. Jamie is to be held in a hidden facility, kept safely out of the way to ensure the Doctor’s continued good behaviour, and Zoe reluctantly agrees to help SILOET fight the Myloki. The forces of SILOET decamp to SKYHOME, and when the City Republic attacks the BFTC, angered by the unprovoked murder of Mark Khan, they find themselves attacking an empty building.
Zoe reluctantly works alongside the other employees of SILOET to get the dangerously antiquated floating fortress back into working condition. However, Bishop realises that she’s trying to bury her hatred of him in her work, and eventually confronts her, concerned that she will put them all at risk if she cracks under the pressure. When given the choice, Zoe chooses not to work alongside Bishop, and he agrees to let her return to the Earth’s surface; however, before letting her go, he asks her for her opinion on the Myloki. When she actually thinks about the problem instead of trying to lose herself in it, it occurs to her to approach the question from a different angle; perhaps the Myloki are closer than they think, hidden behind a rift in reality. Instead of scanning deep space, SKYHOME and Lunar 1 scan closer to home -- but just as they find something, a grid of energy begins to form in the sky, as if enclosing the Earth in a cage...
The Doctor and Storm trace Verdana to a private hospice in Barbados, where his body is slowly wasting away, perhaps due to the hours he spent monitoring the Myloki’s unfathomably alien signals during the war. He is bitter that he’s been condemned to this slow death while Matthews, a jumped-up clerk and chauffeur, became immortal; this is why he wrote the book exposing PRISM. He refuses to help track down Matthews, but when he makes a snide comment about Matthews’ rich friends, Storm deduces where Matthews must be. Storm offers to put Verdana out of his misery, but Verdana refuses, determined to cling on to life until the bitter end. As the Doctor and Storm leave the hospice, Storm admits to the Doctor that he was a mercenary for hire before the war; Bishop freed him from a Polish prison and gave him the authority to kill whoever he had to in order to defeat the Myloki.
Jamie is being held in the underwater facility OCEAN FLOOR, where he bides his time, co-operating until he can get a chance to free the other prisoner he has learned is being held elsewhere in the facility. He is unaware that the other prisoner is Captain Taylor, the indestructible killing machine. When Taylor starts to show signs of life for the first time in 30 years, Dr Koslovski is sent to OCEAN FLOOR to investigate, and when he pops in to check on Jamie, Jamie overpowers him and cuts the bar-code identification out of Koslovski’s hand with a makeshift knife. Jamie then surprises his guards and breaks into the control room, using Koslovski’s ID to get past the automated defences; once inside, he shoots up the control panels before the guards can get in to stop him. He then tries to shoot himself, but can’t quite bring himself to pull the trigger.
OCEAN FLOOR’s warden, Maxwell, leads the guards into the control chamber to recapture Jamie -- but just as he’s come to the conclusion that Jamie has done no irreversible damage, Taylor comes to life and smashes his way out of his concrete prison, which melts around his body. This can’t be Jamie’s doing; the Myloki must have reactivated their agent for some reason. Jamie hides and watches in terror as Taylor smashes his way out of his prison, killing Maxwell and everyone else he encounters on his way past. Jamie eventually works up the courage to follow him out, but on the way he encounters the panic-stricken Koslovski, who is so terrified by the thought of Taylor being on the loose that he fails to notice his security ID has been removed from his hand. Before Jamie can warn him, Koslovski is shot and killed by the automated defences. Jamie then follows the sound of gunfire to find that Taylor has killed the entire crew of OCEAN FLOOR and is preparing to leave in Koslovski’s submarine, the Manta. Finally realising that he’s made a terrible mistake, Jamie leaps into the Manta moments before it launches.
All of SILOET’s attempts to attack the Myloki have come to nothing; even their mini Z-bombs simply disappear when fired at the grid. The grid itself is firing bolts of energy at the surface of the Earth; the Doctor and Storm pass by one of the strike zones, and see that the plant and animal life has been altered into monstrous, twisted alien forms. The Doctor wonders whether contact with this reality damages the Myloki as badly as contact with the Myloki damages this reality, but puts his musings aside for later. He and Storm are on their way to speak with John Sharon, the youngest of the Sharon brothers, who used to run an international rescue team known as Global Response under the leadership of their father, Buck Sharon. Buck always refused to work with the military, but when the war began, PRISM commandeered his resources for the war effort and Professor Dwight “Boffin” Graham, the Sharons’ trusted scientific advisor, went over to PRISM. The bitter Buck Sharon eventually shot himself.
John Sharon, once the wild child of the Sharon family, is now working as a doctor for an isolated tribe in a tropical rainforest. A nearby village was recently struck by a blast from the Myloki grid, and the Doctor chips in to help John tend to those affected by the blast; like everything else touched by the Myloki, however, their bodies have been warped by contact with the alien energy, and the Doctor knows that he can do nothing to save the victims’ lives. John eventually explains to the Doctor that the people of the world turned on Matthews, fearing what he had become, after Verdana’s exposé revealed his secret; Matthews turned to Buck for help, and he agreed to let Matthews hide out on the Sharons’ private island. As far as John knows, Matthews is still there. However, John is torn by conflicting emotions regarding his family and his inability to live up to their shining example, and when the Doctor sees that the photographs of John’s beloved family members have been repeatedly defaced, he realises there’s nothing he can do to help the unfortunate man.
Zoe has decided to remain on SKYHOME after all, but is still torn by the ambiguous morality of working for the people who killed the man she loved. She is also concerned by the fact that the TARDIS has been moved, and as soon as she gets a chance, she investigates discrepancies in the station’s power distribution and breaks into the supposedly disused upper levels, where she meets the eccentric “Boffin” Graham. Somewhat to her shame, she sees a lot of herself in the reclusive scientist. Though he lacks basic social skills, Boffin enjoys discussing his work with a fellow scientist, and to Zoe’s horror, he reveals that he’s developed a device capable of killing the Indestructible Man. Bishop catches Zoe speaking to Boffin and arrests her, but she now knows that he’s using the Doctor to find Matthews so he can kill him. And what will Bishop do with the Doctor once his usefulness is over?
The Doctor and Storm arrive on Sharon Island, where they see a figure striding along the beach -- and when Storm produces Boffin’s device, the Doctor realises what he intends to do and struggles with him for control of the device, attracting the figure’s attention. As the figure approaches, Storm realises too late that it is not Matthews, but Captain Taylor, who has just arrived in the Manta. Storm sends the Doctor to safety, but Taylor kills Storm and then turns his attention to the Doctor. Jamie then arrives and distracts Taylor, and he and the Doctor try to circle around to get Storm’s weapon; however, they are unable to shake off Taylor, an indestructible animated corpse who can do nothing but kill.
At the last moment, Matthews himself arrives and attacks Taylor, and as the two indestructible men fight, Jamie seizes Storm’s weapon and stabs it into Taylor’s back. This time, instead of instantly healing from the injury, Taylor disintegrates into dust. The weapon, which was only ever intended for one use, is destroyed by the blast. Matthews takes the Doctor and Jamie to the Sharon mansion, where the exhausted Jamie explains that he hid aboard the Manta for days without food or water. When he saw Taylor attacking the Doctor, he knew that this must be the real Doctor after all, because the Doctor always fights evil. As Jamie sleeps, the Doctor speaks with Matthews and suggests that the Myloki probes are not weapons, but searchlights looking for Matthews. SILOET troops then led by Captain Drake arrive at the compound to arrest them, and on the Doctor’s advice, Matthews surrenders without a struggle.
The situation is dire. Contact has been lost with Lunar Base, as if part of the Moon has simply drifted out of the solar system; current projections suggest that the Earth will be consumed by the Myloki blight within 27,000 hours; and as Drake returns in the transport KING, the grid begins to power up for a strike on SKYHOME itself. Bishop refuses to evacuate, however, and he forces Zoe to accompany him to the transport deck to witness the end of the war. The Doctor and Drake emerge from KING and try to convince Bishop that his plan will not work, but before they can do so, Matthews emerges from the ship, ready and willing to face his fate. Before the Doctor can stop him, Boffin zaps Matthews with a second device, blasting him to dust.
The Myloki grid seems to power down, and Bishop declares the war over, resigns his post and places Drake in charge, and releases the Doctor and his friends from custody. Bishop and Drake depart to see about closing down operations, while Jamie -- who now has some experience with this sort of thing -- explains to the despondent Doctor that Matthews only came here because he wanted to die. The Doctor sadly explains that the Myloki need to alter the nature of this reality in order to interact with it; the Shiners and Taylor were prototypes, but Matthews was their greatest achievement, half-human and half-Myloki. Unfortunately, the Myloki put too much of themselves into Matthews, and his continued presence in this continuum meant that they could not completely withdraw from it, even though it proved painful to them. They returned to Earth in order to find and remove him, and now, thanks to Bishop, this may be impossible.
The Doctor storms off to confront Bishop, who tries to place him under arrest, refusing to admit the possibility that his plan has failed. However, the Myloki grid then begins to reconfigure itself, and one of SILOET’s best pilots, CHERUB leader Eva Bendix, is transformed into a Shiner and strafes SKYHOME. She is shot down, but Boffin has been killed -- and, to Bishop’s horror, Matthews reforms from dust in the landing bay, still as indestructible as ever. Broken, Bishop allows the Doctor to explain that the Myloki need to take Matthews with them in order to leave this continuum; otherwise, they’ll transform the entire Earth into their sort of reality so they can tolerate its existence. Despite his fear, Matthews agrees to let the Doctor take him up into the Myloki grid and send him into the other reality. Drake arranges for SKYHOME to be evacuated and then raised as close to the grid as it will go; he will pilot the Doctor and Matthews the rest of the way in KING. Jamie and Zoe wait by the TARDIS, which had been taken to Boffin’s laboratory for study. However, Bishop refuses to stand by doing nothing, and he knocks Drake out and takes his place, piloting KING into the energy grid.
In the grid, the Myloki have created a temporary bridge between the two realities, which Matthews perceives as Westminster Cathedral from his childhood memories. Bishop is still hoping to defeat the Myloki utterly, but the Doctor claims that this may not be desirable or even possible. He has come to suspect that the Myloki are literally the opposite of humanity; they embody everything that humanity cannot comprehend about the Universe, and vice versa. The two realities can never truly interact, but neither can exist without the other. Bishop sees his late wife amongst the crowd of tourists, and he vanishes into the crowds, calling out her name. Despite his fears, Matthews then steps into the cathedral, entering the Myloki’s reality; perhaps there, he will finally feel complete.
Back on Earth, Neville Verdana passes away in his sleep as the Myloki energy grid vanishes. The Doctor returns alone to SKYHOME, which is no longer needed and will be allowed to crash in the Pacific Ocean. Drake and the few remaining soldiers evacuate, while the Doctor, Jamie and Zoe return to the TARDIS; their friendship, pushed to its limits, is now stronger than ever.