Before: The Scorpius project has gone horribly wrong. A panic-stricken Paul Hunt manages to break out of his processing unit and get to the communications centre, where he sends a desperate message to the White House begging President Levinson to cancel the project and delete all records that it ever existed. He is then recaptured, and to his horror, the Cyber-Planner reveals that his escape was arranged. Knowing that Levinson would oppose full implementation of the Scorpius project, the Cybermen allowed Hunt to send his warning; now, Levinson will believe that the project has been terminated, and once the time is right, he will be replaced by a new President who will be more amenable to what Scorpius has to offer. Hunt is returned to the processing chambers, and this time, the Cybermen overcome his resistance and convert him into a hybrid: half Cyberman and half human, capable of acting as an undercover agent but wholly committed to the Cyber-conversion of the human race...

Later: Levinson’s successor, Karen Brett, gives in to temptation and uses the teleport supplied by Paul Hunt to travel to Scorpius Base. There, Hunt shows her the Cybermen and explains that they could be the future of humanity, if humanity is willing to surrender the uncontrollable emotions that have held it back for so long. The Cyber-Planner has already “helped” Hunt to overcome his own fear at the prospect. If Brett agrees to their terms, they can begin converting the traitors and political dissidents currently held in the Isle of Wight penal colony into crack cybernetic troops capable of wiping out the androids in Orion. Brett is hesitant at first, but Hunt reveals that he understands the root of her fear: she knows how badly she made the traitor Helliton suffer, and if she’d backed down on Orius Beta VIII and lost the battle instead of torturing him to death for the information she needed, maybe the war would have ended then... and maybe her parents would still be alive. But they aren’t, and she’ll never know whether they suffered as badly as Helliton did. Brett is overcome with grief, loss and despair -- exactly the emotions that Hunt now offers to remove from her...

Now: The refugees from the Isle of Wight have been injected with neural dampening fluid to keep them docile while they’re transported elsewhere for full conversion. However, since Samantha Thorne is an android double-agent, the fluid has had little effect on her. Once the transport ship launches, she emerges from her chamber and tracks down Liam Barnaby, but the fluid has left him unable to process what she’s telling him. Desperate, she pulls him into a deep, arousing kiss, one that wakes his most basic human instincts and gets him thinking again. Still dazed, he vaguely recalls that he’s supposed to hate her for being an android, but he can’t deny that he finds her physically attractive. Sam keeps him aroused long enough to get him to the ship’s computer core, and despite his difficulty concentrating, he manages to reset the hyperdrive co-ordinates just in time. Once beyond Jupiter’s orbital path, the ship jumps through hyperspace, but it doesn’t end up where the Cybermen were expecting it to...

Hunt has written a speech for Brett, and although she vaguely senses that there’s something wrong about it, he now has the means to eliminate the confusion from her mind. Her doubts gone, she addresses the world on a live TV broadcast, revealing the existence of the top-secret Scorpius project. Crack regiments of “volunteers” have been augmented with cybernetic technology and sent into Orion, where they have destroyed key android installations. Soon, the war will be won, but until then, Brett has assigned cybernetic commando units to keep the peace in all major population centres on Earth, in order to protect the people from retaliation by the increasingly desperate androids. Already, Cybermen are walking the Earth, telling the public that there is nothing to fear. All is going according to Hunt’s plan, or so it seems until the Cyber-Planner reports that the last transport ship to leave Scorpius failed to reach its destination...

The Cybermen aboard the transport ship discover that their hyperdrive has been reprogrammed and sabotaged, stranding them in a heavily defended area of android-controlled space. These events are beyond the scope of their programming, and they transmit a report back to Earth, requesting instructions. Meanwhile, Liam and Samantha have fled in an escape pod, and Samantha has transmitted a distress signal to her people; however, Liam points out that even if they pick up the signal, she’s the only one they’ll rescue. As a human, he’s one of the enemy, and he doesn’t expect to be treated well as a prisoner of war. Samantha insists that she’ll convince her people to let him live, but it may be a moot point, as the Cybermen have detected her distress call and are closing in, firing warning shots at the escape pod and demanding that they surrender.

Fortunately, the androids have indeed picked up her distress call, and Riordan has recognised her identification code and taken personal command of the rescue mission. An android perimeter vessel arrives on the scene, and the Cybermen, outgunned, are forced to disengage while they wait for a reply from Earth. Samantha and Liam are taken aboard the rescue ship, where Samantha has Liam sent to the sickbay so the neural inhibitor fluid can be removed from his body and analysed. She reports to Riordan, but is forced to admit that she’s really keeping Liam alive not just for his usefulness, but because she thinks his viewpoint about androids is beginning to change. Riordan isn’t so sure, and he admits that, faced with this new threat, the android war council is considering the extermination of the human race in order to deprive the Cybermen of the organic materials they need to make more of their kind. Samantha is appalled, and Riordan agrees to hold off on this final solution, at least until they’ve captured a Cyberman, analysed its programming, and found out exactly what the Cybermen are up to.

Meanwhile, Liam awakens to find an android doctor, Spavin, removing the neural inhibitor fluid from his nervous system. It’s difficult to do without damaging him, but Samantha ordered Spavin not to harm his patient. Samantha checks in on Liam, and when he learns that she’s about to take a squadron over to the transport ship to capture a Cyberman, he insists upon coming with her; they have a common enemy, and he knows more about the layout of the human spaceship than she does. She decides to trust him, but she’s the only android on the ship who does.

The androids have been jamming transmissions to prevent the Cybermen from receiving new instructions, which is just as well; on Earth, the Cyber-Planner has deduced that the ship must have been sabotaged by an android double-agent, and has transmitted orders to self-destruct so the androids won’t learn the extent of the Cybermen’s plans. The Cybermen on the transport ship eventually realise that the transmissions from Earth are being blocked, but by that time, the androids have beamed aboard. Most of the androids head for the bridge, while Sam takes Liam to the computer core to override the ship’s controls. The androids encounter heavy resistance from the Cybermen, and Liam advises Samantha to call her troops back; she decides to trust him, and once the androids are clear, Liam inverts the ship’s force-field, electrifying the forward section of the ship and stunning the Cybermen. Unfortunately, by this point the Cybermen have decided of their own accord to initiate the ship’s self-destruct systems, and when the androids storm the control room, the disorientated Cyber Leader manages to smash the self-destruct mechanism, preventing Liam from aborting the sequence. With only seconds remaining before the ship explodes, Liam and the androids are forced to retreat empty-handed.

Since contact has been lost with the transport ship, the Cyber-Planner is unable to determine whether the androids have the information they require; it thus decides to assume that they have, which means the Cybermen must move their master plan forward. Brett’s approval ratings have risen significantly since her speech, and she now gives a final speech to her people, declaring world-wide martial law and announcing that she will personally lead the final assault against the androids in Orion. Once she has finished speaking, she returns to Scorpius, where she undergoes complete Cyber-conversion. Karen Brett has finally lost all of her humanity and become a Cyber Leader. She and her taskforce depart from Earth in the advanced XP-900 warship, which has itself been augmented with Cyber technology. But they aren’t going to Orion...

Liam awakens aboard the androids’ ship to learn that he beamed out at the very moment the transport ship exploded; fortunately, the last of the neural inhibitor fluid in his brain saved him from a serious concussion. However, the remains of the transport ship have depressurized, and all of the humans aboard are dead. Prime Riordan himself arrives to interrogate Liam, and although Samantha insists that Liam is responsible for saving their lives, Riordan remains hostile towards Liam... as if he’s jealous. But as debris from the transport ship begins hitting the sickbay window, Liam unexpectedly bursts out laughing; against all the odds, a Cyberman’s decapitated head has drifted across space and struck the android ship. The androids pull the head in and scan its cybernetic memory circuits, and within, they find a map of the galaxy, containing the locations of over a thousand planets on which Cyber hibernation vaults have been hidden. The master vault is located on the planet Telos, and if it is activated, then billions of Cybermen will awaken throughout the galaxy, spelling the end for humanity and androids alike. The androids must get to Telos before the Cybermen do.