Continuing from the events of the previous episode; the Torchwood team split up; heading for different sites around the city. Gwen and Rhys go to the police station after PC Andy informs Gwen that senior officers have been murdered by Weevils. Tosh and Ianto go to the Central Server Building to deal with "Ghosts" that have appeared, killing them easily. Owen heads to St. Helen's Hospital, where a Hoix has been found chewing on cables and using a packet of cigarettes, he lures it, sedating it with a syringe.
Jack returns to the Hub, finding John Hart playing "I Lost My Heart to a Starship Trooper", referring to it as 'their song'. After a brief conversation; John confesses his love and shoots Jack to death. When Jack revives; he is chained up and stripped of his weapons as he watches John carry on with his task. John instructs the team to head to their roofs as he blows up parts of Cardiff city. This not only separates them further; but leaves each team member to deal with more mayhem. As Jack watches the city crumble; John transports them both back to Cardiff 27 AD.
John explains that his actions were involuntary and that his wristband is equipped with surveillance and detonation circuits, molecularly bonded to his skin. Before he can explain any further; Jack's brother Gray arrives and drives a blade through his brother's ribs. Gray explains his hate and resentment for Jack for leaving him behind, which led to his torture as a child. He forces John to bury Jack. John throws a ring into the grave, claiming its sentimental value, then buries Jack alive.
John returns to present day Cardiff to help the team. After confrontation with Gwen, he orders Tosh trace the ring as it is in fact, a detector. Whilst John and Gwen try to trace the ring; Gray releases the Weevils, sending them into the street; preventing Tosh and Ianto from reaching the nuclear plant to stop the meltdown. Owen goes to stop the meltdown instead as he still controls the Weevils and he is closer to the plant.
Tosh and Ianto arrive and shoot the Weevils surrounding John and Gwen, but Tosh remarks that a bullet won't kill them so the others return them to the cells. Gray traps them in the cells while Tosh helps Owen to stop the meltdown. As she is doing so; Gray shoots Tosh in the stomach before leaving her for dead after hearing a loud noise. As Gray follows the noise to the morgue; he opens one of the chambers to find Jack awake. It is revealed that Jack was discovered in 1901 by Torchwood personnel as they detected John's ring. They placed him in the cyrochamber with a timer set to wake him up in present day.
Jack asks for Gray's absolution after forgiving him for his burial, but Gray refuses saying his hate is too deep. Jack chloroforms Gray while John recalls the Weevils from his cell. Jack frees Ianto, Gwen and John, thanking him for his help. While this has been happening; Toshiko who is bleeding to death, continues to help Owen at the nuclear plant. Owen guesses that something is wrong but Tosh reassures him it's just her broken arm.
Tosh and Owen avert immediate meltdown by venting the flow channels into the control room Owen is in, with a time delay set so that Owen can escape. However, emergency lockdown is triggered after a power strike hits the plant; trapping Owen. Both bound for death, they talk, and Owen apologises for not realising his feelings for Tosh and never being able to go on a date. The radioactive material flows into the control room and Owen remarks that 'it's alright', before the scene fades to white.
As Tosh sits helpless to save Owen; Jack notices blood on the floor and finds her weakly propped up against the chair. While Gwen injects her with a pain-killer; Tosh explains Owen's situation to everyone's dismay. Tosh weakly smiles up at Jack, who smiles back; and dies in his arms, a tear running down her cheek. Both he and Gwen cry and as he hugs Tosh's body; the scene fades to Gwen's flat where she and Rhys are watching news coverage, devastated.
Jack freezes Gray and John suggests killing him as his disturbed state is less likely to change. Jack refuses stating that 'there has been enough death'. He also mentions that his burial was penance. John, deciding to explore Earth further, kisses Jack before offering his sympathies and leaving.
As Ianto performs the final log-out procedures for Tosh and Owen; Gwen and Jack pack up their stations, heartbroken. As Toshiko's death is registered; a pre-programmed video made by Tosh appears in which she says her goodbyes and confesses her love for Owen. She thanks Jack for saving her from UNIT and showing her the wonders of the universe before the video ends. Gwen remarks that she cannot go on without them but Jack reassures her that they can because 'the end is where they start from'. The episode ends with Jack, his arms around Ianto and Gwen in tears inside the Hub, and an overhead shot of Cardiff Bay.