At Torchwood, Jack, Gwen, Owen, and Tosh are playing indoor rugby. Ianto arrives as they finish up and go out for drinks. Once they’ve left, Dr. Taniziki arrives and Ianto lets him in. Ianto takes Taniziki to the basement storage area and shows him his secret: a woman, partially converted into a Cyberman. Ianto kisses her gently on the cheek.
Taniziki, a cyberneticist, is impressed and surprised to see that one of the Cybermen survived. Ianto explains that the woman, Lisa Haller, worked for Torchwood in London during the Canary Wharf battle. The Cybermen began converting bodies rather than transplanting brains, and Lisa was only partway through the process when Ianto pulled her out. Taniziki catalogues the percentage of change that Lisa has undergone. Ianto explains that he took units from a cyber-conversion pod under Lisa’s guidance. Lisa wakes up and Taniziki runs some tests as Lisa explains that Ianto is her boyfriend.
Taniziki and Ianto take Lisa to an upstairs lab and the cyberneticist prepares to remove her from life support. He warns that there is a risk Lisa will die and begins the procedure.
Jack and the other staff are drinking at a bar when they get word of a UFO sighting over Cardigan Bay. Jack orders them back to base.
Ianto starts to threaten Taniziki with what will happen if Lisa dies, but Lisa wakes up and starts breathing on her own. Taniziki warns that it’s only the first step. Ianto picks up a signal that the Torchwood crew is coming back and he and Taniziki get Lisa up. She insists on walking on her own and the two men help her downstairs. Once they’re in the storage room, Ianto goes back upstairs to check on the others.
In the storage room, Lisa grabs Taniziki and slams her down on to the conversion table. She then activates the conversion mechanism and Taniziki looks up in horror as blades descend toward his face. Lisa insists that the human race is weak and she can make Taniziki strong.
In the Hub, the power goes down and Jack orders a system diagnosis. Ianto leaps in and says that he had generator problems earlier and he’ll go to fix it. He runs downstairs and discover Taniziki, dead, his face partially merged with cybernetics. Lisa insists that she can deal with Torchwood and Ianto tells her not to go near them. He figures that something has happened to her mind. When he snaps at her, she starts to advance on him before he notices. When he reverts to sympathy, she stops. Ianto tells her to rest while he disposes of Taniziki’s body. As he leaves, he tells Lisa that everything will be okay. Once Ianto is gone, Lisa reactivates the conversion pod.
The Torchwood team warns the UFO crew off and the power goes off. Jack tries to contact Ianto, who is busy moving Taniziki’s corpse.
Lisa feeds more power into her cybernetic body and smiles in triumph.
Tosh discovers that there are two human life signs in the basement, the source of the power loss, and Jack concludes that they’ve been invaded. He orders battle protocols and Gwen and Owen go to the basement to find Ianto. They lose contact on the radio due to the power surge. While Tosh tries to reestablish contact, she discovers that someone has tampered with the security footage. She’s able to bring up footage of Taniziki meeting with Ianto inside of the facility.
Gwen and Owen enter the storage room and Owen recognizes the equipment as Cyber-technology. Gwen shuts it down and the power resumes. Tosh and Jack contact Gwen, who informs him what they’ve found. Jack orders them back up but Lisa steps out and knocks out Owen. Jack goes to help and tells Tosh to activate shutdown and get to safety. Below, Lisa advances on Gwen and easily disarms her, and then places her in the conversion unit. Jack arrives and shoots at Lisa, but Ianto grabs him and throws off his aim. Lisa walks off while Ianto and Jack try to free Gwen. They have no choice but to tell Tosh to cut off the power, initiating a total lockdown. Ianto apologizes and Gwen wonders why. They free Gwen head back up with the unconscious Owen. They spot Lisa, who walks away before they can shoot. Jack points his gun at Ianto, realizing that he’s involved.
In the Hub, Jack orders Tosh to get to the weapons and then demands answers from Ianto. Jack demands to know what else he’s hiding and Ianto notes that Jack has never cared about his personal life. Ianto explains that Lisa is his girlfriend and Torchwood exists to destroy alien threats: he wasn’t going to tell them about her. Jack warns him that there is no cure and anyone who is converted stays that way. Ianto insists that Lisa wasn’t totally converted but Jack warns that Cyberinvasions begin with one human who they exploit. They then spread, wiping out worlds and assimilating populations. Ianto refuses to give up on Lisa and Jack tells him to figure out which side he’s on.
Lisa enters the chamber and Ianto goes to talk to her. She insists that the army will be rebuilt inside of Torchwood and identifies herself as Human Point Two. Jack points out that she’s not a Cyberman yet. Lisa looks at her reflection and says that she’s disgusting. She insists on starting again and upgrading properly. When Ianto explains that he brought her there to be together, Lisa suggests that they transplant her brain into his body to become one complete person. When Ianto refuses, she states that they’re not compatible and throws him aside. The team splits up and tries to keep Lisa distracted, and then regroup in the conference room. Jack gives a lock descrambler to Tosh and tells her to go up the emergency stairs to reception, and patch emergency lights into a specific circuit. He then has Owen and Gwen go to the autopsy room to find weapons while he buys them time.
Jack taunts Lisa and runs back to the Hub. Tosh uses the device to open the gates and the main door while Lisa grabs Jack and electrocutes him. She leaves him dead on the floor and advances on Tosh. Tosh gets the gate open while Jack gets back to his feet. Lisa electrocutes him again, killing him once more. Tosh manages to get out just in time.
Gwen and Owen get to the autopsy room but Lisa advances on them. There’s no exit out and Owen figures they have to hide in one of the drawers. The two of them have no choice but to lie on top of each other. As Lisa searches the room, Jack revives and gets Ianto clear. As Gwen and Owen listen to Lisa close in, Owen decides to kiss Gwen. Meanwhile, Jack administers mouth-mouth to Ianto, reviving him.
Lisa gets ever closer to Gwen and Owen. Gwen’s phone rings: it’s Kai Owens, asking her to video wife-swap. Gwen and Owen get out of the drawer and Lisa advances on Gwen. Owens attacks her with a knife, stabbing her through the partial armor plating. Gwen wonders what Owen was up to and Owen tries to dismiss it, claiming it was a last kiss for the condemned man. He notices that she didn’t put up much of a struggle. Ianto arrives and looks down at Lisa… who wakes up and advances on them.
As Tosh tries to reroute the power, Jack grabs a blowtorch and a bottle of liquid. He tries to hold her off but Lisa is content to wait until the power runs out. Ianto begs Jack to save Lisa, but Jack tells the others to hold Ianto back while he sprays Lisa with the fluid. He explains that it helps the pterodactyl identify its food. It flies down and attacks Lisa, while Tosh gets the power working. The lift activates, lifting the team up towards the surface. Below, the pterodactyl rips open Lisa as the woman screams in terror and Ianto looks on in horror. Tosh meets them in the plaza and Ianto slugs Jack, accusing him of abandoning Lisa. Ianto insists that Jack is worse than anything they have locked up, and that one day he’ll stand aside as he watches Jack die. Jack insists that killing Lisa was the only way. Tosh tells them she tripped the lockdown timer and they should be able to get back in.
As the team runs back to the headquarters entrance, Annie the pizza girl arrives. The doors open and she walks in and down the stairs. The floor of the Hub is covered in blood. Annie is unaware that Lisa is behind her.
The team gets back inside and Ianto grabs a gun, telling them he’ll shoot anyone that interferes. Jack disarms him and holds the gun to his head. He tells Ianto that if he goes back in, it’s to finish the job. If Lisa is still alive, Ianto will have to execute her. Ianto refuses and Jack tells him that it’s time to stand as part of the team. If Ianto refuses, Jack says he’ll shoot Ianto and Lisa. Ianto refuses and Jack gives him ten minutes to deal with Lisa. Ianto takes a gun and goes downstairs.
Ianto enters the Hub and sees the discarded pizza box. The base is undergoing another power loss and Ianto follows the trail of blood to the storage room. He finds Lisa, dead. As he cries in grief, a figure steps out of the shadows: Annie. “Annie” explains that she’s Lisa: she transplanted her brain into the pizza girl’s body. Lisa says that Ianto fought so hard for her, she couldn’t let herself go. She describes in great detail their times together and asks him to hold her and tell her that everything is all right. Ianto embraces her, crying, and then points the gun at her head. Lisa pleads with him to stop, saying she did it all for him. Ianto apologizes, but then drops the gun. As he turns away, Lisa says that they can be upgraded, together. The others arrive and open fire, killing her.
Later, Ianto arrives to clean up the base. He looks up at Jack in the conference room, silently asking for permission. Jack nods and Ianto goes to work. Gwen asks Jack if she would have shot Ianto, or shot her if she’d stood by Ianto. Jack doesn’t directly answer her question. She wonders if Ianto will stay after losing his beloved, and if Jack has ever loved anyone that much. Jack doesn’t say anything. Gwen notes that when she saw Lisa killing him, she wondered if he could really die. Jack admits that he wondered the same thing, and that he felt more alive than ever in that moment of time.