Ianto Jones appears nervous as he enters the Hub and watches the rest of his colleagues engaged in a game of basketball. The group are taking the opportunity to unwind a little and Owen and Gwen eventually win the game, despite accusations from Jack and Toshiko that their last move was illegal. Ianto waits for them to enter the lift and as soon as they’re out of sight, he races downstairs. Unaware of their friend’s strange behaviour, the others cross Cardiff Bay waterfront and discuss the merits of taking Jack to his first rugby tournament.
Ianto phones the local pizza delivery shop and orders two pizzas. Just then, the main entrance to the Hub opens and an elderly Japanese man enters. Ianto rushes over to greet Dr Tanizaki and then leads him downstairs into a previously unseen section of the cellar. They head towards a strong set of doors which Ianto cautiously unlocks. They enter a large room set up like a surgery and approach a beautiful woman on a life-support system strapped to a metal framework, like an operating table. Dr Tanizaki is amazed to see she is mid-way through conversion into a Cyberman! Ianto leans over the woman and gently kisses her.
As Ianto introduces the woman as Lisa, her eyes open - but he assures Dr Tanizaki this is just a reaction to her medication. Realising she is the only survivor of the Cyber-race left anywhere in the world, Dr Tanizaki thanks Ianto for allowing him to study her. Ianto explains that he and Lisa worked for Torchwood 1 in London. At the end of the Canary Wharf battle, the Cybermen needed reinforcements fast so they started upgrading whole bodies instead of just transplanting brains. Lisa was half way through the process when the machinery shut down. Ianto pulled her to safety and brought her here. Dr Tanizaki examines Lisa and realises she‘s been considerably augmented - for example her breathing and hearing appear to be completely cybernetic - but about 40% of her body remains human. Ianto asks whether he can make her human again. Dr Tanizaki is wondering how Ianto was able to modify the life-support system from Cyber technology when Lisa wakes up and explains that she told Ianto what to do. She is pleased that Ianto kept his promise to bring a cybernetics specialist here to help her. Lisa tells Dr Tanizaki she is 26 and the last thing she remembers before coming here was pain!
Dr Tanizaki and Ianto move Lisa upstairs to examine her condition in more detail. Their first step is to remove her from the respirator so she can breathe unaided. Ianto is shocked when the doctor tells him he must be prepared for her not to survive. They switch off the life-support and Lisa immediately starts to flatline…
Jack and the others are enjoying each other’s company in a nearby bar when they receive an alert telling them of a UFO sighting over Cardigan Bay. The emergency services are already on their way, so Jack gives them ten seconds to finish their drinks. As they cross the Bay, Owen and Toshiko start arguing about who should be allowed to drive the car and Gwen diplomatically suggests drawing up a rota.
Lisa revives and starts breathing normally and Ianto is delighted. Suddenly an alarm warns him that the others are heading back towards the base. The two men quickly detach Lisa from the monitors and Dr Tanizaki helps her walk back downstairs while Ianto races to clear up any evidence of what they’ve been doing before his colleagues return. He then joins them in the cellar and tells them he’ll return once the others have gone again.
Back in the Hub, Jack assigns duties to each of the group including speaking to Neil, a man at Jodrell Bank with a voice like Sean Connery, and to the RAF, just in case the UFO turns out to be a case of mistaken identity. Ianto joins them and does his best to act normally. Downstairs, Dr Tanizaki helps Lisa back to the surgery - whereupon she suddenly regains her strength, grabs him by the throat and lifts him several feet off the ground! She attaches him to the operating table and, ignoring his cries for help, she activates a control which opens up a hatch above Dr Tanizaki’s head, revealing surgical equipment…
In the main Hub, the lights start to dim and the monitors indicate a power drain. Toshiko starts to run a systems diagnostic but Ianto intervenes and says he experienced some generator problems earlier in the evening. He tells them some cabling had come loose, but he thought he’d fixed it. He offers to go back down for another look. Away from the others, Ianto races down the cellar corridor and into the surgery where he finds Lisa standing over the dead body of Dr Tanizaki. He’s covered in blood and has clearly had some major surgical work which has left him disfigured and with bits of machinery emerging from his face. Lisa tells him the upgrade failed and he realises she did this deliberately. She wanted to repay him by removing the weakness of his humanity. He convinces himself that she’s suffering from some sort of post-traumatic disorder as a side-effect of the conversion process, but he starts to panic, realising that the others are bound to found out what they’ve been doing. He tells her to stay hidden and rest while he tries to dispose of Dr Tanizaki’s body.
In the lab, Toshiko is showing the others footage of the UFO which Jack identifies as a first-generation leisure-crawler belonging to a race of aliens made up mostly from liquid. He tells Toshiko to send a message warning them away as they’re spooking the locals. Gwen wonders whether they should be interrogating the aliens, but Jack says they’re so boring it would take a month just to ask the first question. At that moment, there’s another 23% power drain and Jack tries to contact Iago to check whether he’s found the problem - but Iago is busy dragging Dr Tanizaki’s body through the corridor. In the surgery, Lisa has attached herself back to the metal framework and is recharging herself with electrical energy.
The power drain reaches 30% and Toshiko identifies the source as coming from the storeroom at the bottom of the building. She does a scan for heat signals and picks up two life-forms in the cellar. Jack concludes they’re under attack and orders them to assume battle protocols. The group arm themselves and Owen and Gwen volunteer to go down to the cellar. While Ianto is hiding the body in the cells, Owen and Gwen arrive in the corridor and approach the storeroom. The power drain reaches 50% and Jack loses communication with the others. Meanwhile, Toshiko has been checking the internal CCTV footage and has discovered that several sections over the last couple of hours have been deliberately deleted. She manages to dig deeper into the system and she and Jack watch on the screen as Ianto greeted Dr Tanizaki on his arrival. Ianto’s treachery has been revealed!
Through a panel, Owen and Gwen can see the operating table but can’t make out enough detail, so they have no choice but to go inside… Owen identifies the equipment and orders Gwen to switch it off. When the internal power is restored, he Owen tells Jack that they‘ve discovered a fully powered Cyber-conversion unit. He explains that the Cybermen brought down Torchwood 1, but they were believed to have been destroyed. Jack instructs them both to come back upstairs immediately, but before they can move Owen is knocked unconscious by Lisa. Gwen tells Jack they have a Code Zero Incursion - they’re under attack - and Jack instructs Toshiko to implement total shutdown procedures and get herself to safety if she hasn’t heard from him in fifteen minutes. If they have a Cyberman on the base he needs her to act as last line of defence to make sure it never gets to the outside world.
Gwen tries to hold Lisa off at gunpoint, but the Cyberwoman quickly disarms her and forces her onto the operating table. She tells Gwen she will be like her and starts to activate the conversion process. Jack arrives and opens fire on Lisa, but his aim is deflected by Ianto. As the two men struggle, the surgical equipment descends from the hatch above Gwen and she cries out for help. Ianto tries to switch off the power, but nothing seems to work. Jack calls Toshiko and orders her to cut off all the power in the base even though this will mean the Hub goes into lockdown and they’ll all be trapped inside. They have no other option, so she pulls the lever and all the lights go off and the doors around the base slam shut and lock.
The Cyberwoman has gone, so Jack orders Ianto to stand guard by the door while he releases Gwen. The three of them slowly make their way back through the basement corridor, with Jack carrying the unconscious Owen. Before they can make it back to the stairs, Lisa appears from the shadows and blocks their path. Jack admits that he doesn’t know what to do - but then Lisa turns and moves off. A furious Jack puts a gun to Ianto’s head and demands he get them back to the Hub safely.
They return to the main lab and Toshiko tells them she can’t access the weapons store as it’s been locked down along with the doors. Jack orders Ianto to his knees with his hands above his head. He demands answers and Ianto admits that he brought the Cyberwoman to the base. When Jack reacts badly to this news, Ianto points out that although he clears up after them, no one has ever taken any interest in his personal life. The Cyberwoman is Lisa, his girlfriend, and he didn’t ask for their help because Torchwood exists to destroy alien threats. His loyalty is to her, not the group, but Jack points out that there is no cure for what’s happened to her. What Ianto has done could lead to mass slaughter, allowing the Cybermen to regain a foothold on this world by exploiting his human weakness. If they rebuild their forces, their race can spread out across the Universe, erasing worlds and assimilating whole populations. Jack demands they work together to stop this, and although Ianto insists Lisa’s conversion was never completed, Jack reminds him that she’s already tried to kill Gwen. But Ianto loves Lisa and won’t give up on her.
Toshiko has established that it will take another six hours for the power to come back online. At that moment, Lisa arrives in the lab and Ianto approaches her. Lisa announces that this building is suitable and the Cyber army can be rebuilt from here. Jack tells her to look at her own reflection and Lisa realises that her upgrade was not complete. Finding herself disgusting, she plans to start again, upgrading herself properly. Ianto tries to convince her that he brought her here to cure her, so they could be together - and she decides to transplant her brain into his body so they can be fused together into one complete person. Ianto breaks down in tears. Realising they are not compatible, Lisa grabs Ianto by the throat and hurls him across the room. Jack tries to shoot her, but she returns fire with an electrical charge.
Jack orders everyone to split up and when Lisa marches towards Gwen, Owen tries to distract the Cyberwoman by drawing her attention. The group reassemble in the boardroom and Jack reminds them they’re engaged in a fight to the death and they must do whatever is necessary to destroy the woman. Jack gives Toshiko a device that Suzie Costello found last year that can open any lock in 45 seconds. He tells her to escape through the emergency gate and go up to the main reception area. Once there, she needs to open a panel near the desk and patch in a circuit from the main system and use it to power some portable devices he hands her. In the meantime, Jack will try to buy Owen and Gwen enough time to find something they can use as a weapon. Owen suggests they try the autopsy room and the group splits up again.
While the others escape, Jack draws Lisa in into the boardroom and they circle each other around the table before Jack is able to get back out. She follows him downstairs and declares the building is hers now. Jack challenges her and she grabs him by the throat and he is instantly killed with an electrical charge. Gwen tries to help him, but Owen holds her back. Lisa then turns her attention to Toshiko who has successfully used the device to open the security gate. To everyone’s surprise, Jack recovers and gets back on his feet - but Lisa grabs him again and kills him a second time. The Cyberwoman then returns to Toshiko who is now trapped between the gate and the main entrance. She uses the device again and there is a race to get the entrance open before Lisa can break through the security gate. She manages to get through just in time and although Lisa smashes her fist through the glass porthole, Toshiko is safe for now. She races upstairs to the main reception area.
Owen and Gwen race into the autopsy room and begin searching for suitable weapons. Lisa spots them and abandons her attempt to get to Toshiko. With the Cyberwoman striding towards them, Owen and Gwen desperately look around for a hiding place. Their only option is to climb inside one of the small storage lockers. Lisa arrives and searches in vain for her prey. Inside the storage area, Gwen is lying on top of Owen when he grabs her and gives her a long kiss. Lisa stands in the room listening for any noise, but there’s nothing so she starts looking inside the lockers. Just then, Gwen’s mobile phone rings. It’s Rhys on the other end, explaining that he’s going for a curry with his mates and asking Gwen to tape “Wife Swap” for him. Lisa heads straight for the locker and Owen and Gwen burst out and try to get to safety. As Lisa approaches Gwen, Owen grabs a surgical instrument from a tray and plunges it straight into the Cyberwoman’s stomach.
Jack recovers again and drags Ianto’s lifeless body to one side. He tries to revive him, but there’s no reaction so he gives him the kiss of life. Ianto slowly recovers and then jumps to his feet when they hear the distorted electronic scream coming from Lisa. Owen and Gwen catch their breath as Lisa collapses to the floor, apparently dead - then Gwen demands to know why Owen kissed her! He assures her it was just a last kiss for a condemned man, and he’s embarrassed now that they haven’t been killed. Ianto races over to Lisa while the others tell him they had no choice, it was kill or be killed. But Lisa is not dead and he eyes snap open. The three of them flee for their lives, with the Cyberwoman following close behind again.
Owen wants to know why Jack isn’t dead, but the response he receives is vague. Instead, Jack prepares a blow-torch and tries to fend off the approaching Cyberwoman. However, Lisa knows the power will run out eventually and she’s prepared to wait. Ianto demands they give her a chance to surrender, but Owen and Gwen hold him back while Jack squirts an alien-looking liquid over Lisa. He explains that this helps their pet pterodactyl identify its food! Jack, Owen, Gwen and a struggling Ianto stand together on the elevator-stone as the pterodactyl flies down from the rafters and heads for its prey.
Upstairs, Toshiko has dismantled a control panel under the desk and is desperately searching for the circuits she needs to power Jack’s portable devices. She’s successful just as the pterodactyl attacks Lisa. The others slowly start to ascend to ground level on the elevator-stone and watch as the Cyberwoman puts up a valiant defence against the dinosaur. As they approach the roof of the Hub, the last thing they see is the motionless body of Lisa, apparently being ripped apart by the giant bird.
As the group emerge onto Cardiff Bay they are joined by a relieved Toshiko. Ianto is inconsolable and he lands a punch on Jack that knocks him to the ground. He accuses Jack of being worse than anything they’ve faced. One day he hopes to have the chance to save Jack and will sit back and watch him die! Owen and Gwen separate the two men and Toshiko explains that she was able to restore the power, which should be coming back on any moment. Knowing he can get back in, Ianto runs off before anyone can stop him. The others give chase…
At the main Tourist Information office, the pizza delivery girl Annie arrives with the order Ianto made earlier. She rings on the door, which opens of its own accord. Entering the office, she moves through the doors as they automatically open and eventually she finds herself downstairs in the main Hub. She’s amazed by the scale of the laboratory - and the sound of a strange creature flying above her - but fails to notice the form of the Cyberwoman standing behind her.
Ianto races into the main reception office and reaches the inner door before the others catch up with him. He pulls a gun on them and tells them he has nothing left to loose. He plans to go back in to save Lisa and if anyone tries to stop him, he’ll shoot them. Jack is able to disarm him and pulls his own gun on Ianto. He tells Ianto that if he’s going back in, it has to be to finish off the job! If Lisa is still alive, he must execute her. Ianto refuses and Jack reminds him how he betrayed the team. The girl he loved has gone and his loyalty should be to them now. Ianto still refuses and calls Jack the biggest monster of all. Jack gives him ten minutes to kill his girlfriend and if he hasn’t done it by then, he’ll go in himself and kill them both.
Ianto returns alone to the Hub and sees the discarded pizza boxes and the floor covered in blood. The lights start to dim as the power drains away and he realises what’s happening. He races down the basement corridor and bursts into the surgery - only to find Lisa’s body lying motionless on the floor. He examines her and discovers she’s dead. As he breaks down in tears, a girl’s voice calls his name. He looks up in shock and sees the blood-stained pizza delivery girl. She emerges from the shadows to reveal a deep bleeding scar running across her forehead - evidence that she’s recently undergone an operation. She explains that she is Lisa, and is human again. She has taken Annie’s body and transplanted her own brain into it. At first Ianto isn’t sure, but Lisa/Annie recounts moments from their life together that only his girlfriend would know. Once again he is inconsolable and they hold each other silently.
After a moment, he steps back and holds the gun to her head. She begs him not to hurt her and tells him she did this for him so they could be together. He can’t bring himself to shoot her and turns away. As she tells him they can both be upgraded, she is suddenly hit by a barrage of bullets. Jack, Owen, Gwen and Toshiko all continue firing shot after shot until her dead body is flung back against the metal operating table. Ianto looks at his friends with a mixture of shock and contempt, then he returns to Lisa’s original body on the floor and falls to his knees.
Much later, Ianto returns to the main Hub. He looks up at Jack who is watching him from the boardroom and there is the faintest of nods from them both. Gwen tries to convince herself that Jack would never have shot Ianto, but she wonders whether he’d have shot her too if she‘d been in that position. They watch as Ianto moves around the Hub, clearing up as much of the mess as he can. They’re not sure whether Ianto will want to stay. Gwen asks Jack whether he’s ever loved anyone as much as Ianto loved Lisa but she gets no answer. His only response is to tell her that when Lisa electrocuted him, he actually thought he might die - and just for a second, he felt really alive.