Following the previous episode directly, the Torchwood team goes to a site of rift activity. Gwen goes to the police station where the four most senior officers have been killed by Weevils. Tosh and Ianto head to the central server building to deal with "ghosts" that appeared in the building. The ghosts turn out to be humanoid beings in cloaks holding scythes who look very like the Grim Reaper, but Tosh and Ianto easily end the threat by shooting them. Tosh mentions that the server building houses servers for the military, police, NHS and the nearby nuclear power station. Owen heads to St Helen's Hospital where a Hoix was found chewing on cables and subdues it with a sedative. With the rest of the team away dealing with their respective crises, Jack returns to the Hub alone and encounters John Hart, who after a brief conversation with Jack, kills him, then strips him of his weapons and restrains him while he proceeds with his task.
John gets the Torchwood members to approach the rooftops of their respective buildings to watch as he sets off 15 major and well placed explosions in Cardiff. The team try to cope with the workload of a crippled city. John, who is watching the mayhem in Cardiff Castle with a captive Jack takes him through the rift to the future site of Cardiff city in the year 27 AD. There John explains that he has not been acting of his own free will and shows Jack that his wristband has been molecularly bonded with his skin (rendering it unremovable) which is equipped with surveillance and remote detonation circuits to ensure his obedience. Before John can explain further he is interrupted by the arrival of Gray, Jack's long lost brother. Jack hugs him tearfully, happy to see him alive, only to have Gray stab him in the chest. When Jack comes to, Gray explains that he was tortured mercilessly for years by the aliens who captured him in his childhood, and that he blames Jack for what he had to endure. Gray taunts Jack saying that his grave will be the foundation of Cardiff and that his blessing of life is his curse. He then forces John to bury Jack alive as punishment for this. Before he begins his task John throws a ring into the grave, claiming that it is of sentimental value. He then proceeds to fill the grave, trapping Jack in a cycle of asphyxiation and revivification.
John, now gone free and released from his obligation to Gray, returns to the present to help undo the mess he caused. Gwen encounters him and they call everyone back to the Hub except Owen, who is trying to contain the nuclear power plant meltdown--a result of the explosions John had previously set up. Unbeknownst to them, Gray is lurking in the Hub with them. He first releases the Weevils with a signal, flooding the streets of Cardiff with them, and eventually traps Gwen, John, and Ianto in Weevil cells, and then shoots Toshiko, leaving her for dead. A loud banging noise is heard by everyone and Gray goes to investigate. The sound leads him to the morgue where a light can be seen coming from one of the compartments. Gray opens the compartment to find Jack waking in a cryochamber.
The scene then flashes back to 1901 where Jack is discovered by Torchwood personnel because the ring that John dropped was in fact a beacon and Torchwood had picked up the signal. They dig him out and place him in the cryochamber at the Hub, with a timer set to wake him up in 2008. Forgiving Gray for burying him, Jack requests that he do the same for him, but Gray says that as his hatred of how Jack left him behind is what keeps him living, he cannot absolve his older brother; Jack sorrowfully chloroforms Gray. Meanwhile, Captain John successfully sends out a 'recall signal' for the Weevils, causing them to return to the sewers; Jack then frees Gwen, John, and Ianto. While this has been happening, Toshiko had been helping Owen to try to prevent a meltdown; despite her life-threatening injury. After successfully averting disaster by venting the flow channels into the room Owen is in, she also sets a time delay so Owen can escape. However, a power spike triggers an emergency lockdown and Owen is trapped. Toshiko and Owen, who are both bound to die talk for a while but before long the radioactive material is sent to Owen's location and the scene fades out back to the Hub. Jack discovers Toshiko who dies in his arms.
Jack places Gray inside a cryogenic chamber; due to Gray's damaged and disturbed mind John suggests killing him, but Jack says "there has been enough death". John mentions to Jack that he didn't struggle as John shovelled the dirt over him, with Jack responding that it was his penance. John informs Jack that rather than go back through the rift, he'd like to see a bit of Earth and maybe he'll see him around sometime.
As Ianto registers Owen and Toshiko's deaths on the Hub computer, a pre-programmed pop-up video of Toshiko appears, in which she says goodbye and confesses her love for Owen and the rest of the team, as well as thanking Jack for freeing her from the UNIT prison and showing her the many possibilities of the universe. The episode and second series closes with the devastated city recovering, and Jack, Ianto, and Gwen standing together in the Hub.
John Barrowman – Captain Jack Harkness
Eve Myles – Gwen Cooper
Burn Gorman – Owen Harper
Naoko Mori – Toshiko Sato
Gareth David-Lloyd – Ianto Jones
James Marsters – Captain John Hart
Lachlan Nieboer – Gray
Kai Owen – Rhys Williams
Paul Kasey – Weevil / Hoix
Tom Price – PC Andy Davidson
Paul Marc Davis – Cowled Leader
Golda Rosheuvel – Dr Angela Connolly
Syreeta Kumar – Nira Docherty
Cornelius Macarthy – Charles Gaskell
Amy Manson – Alice Guppy