End of Days (TV story)

Plot
Gwen has been watching Rhys sleep and after some banter, she asks him to make tea. He kisses her and makes off, Gwen noting his "nice arse." Gwen answers her phone—Jack asks if she’s seen the news. In the living room, Gwen and Rhys are watching chaos unfold on the television. UFOs have been sighted over the Taj Mahal and police have clashed with English civil war era soldiers. The two speculate, Gwen concluding it can’t be an act of terrorism—terrorists use bombs, this is different.

At the Hub, Ianto recites biblical verses from the King James Bible, Daniel 12:8-9 (though he says it is 12:10). Jack cuts in as he moves onto an apocalyptic text on Abaddon the "great devourer," remarking how mankind is obsessed with anything that "denies the randomness of existence."

Institutions across the globe (including UNIT) have their eyes trained on Torchwood and the team question their responsibility. Running a simulation, Toshiko demonstrates how the rift—or more specifically, Torchwood 3—is the epicentre of all the temporal incidents. The rift is expanding and history is falling through the cracks. Jack is quick to put the blame on Owen who justifies opening the rift to save Jack and Toshiko. Gwen clashes with Jack over putting Owen on the spot. Jack departs, bitingly remarking she'd know all about Owen's feelings.

Jack has instructed Owen and Toshiko to investigate a quarantined hospital where they find the bubonic plague has broken out after the admittance of a plague victim from the 14th century, the time of the Black Death. Owen instructs the woman's doctor in what medicine to give her, and when the doctor answers in surprise that this is the standard medicine against plague, Owen warns the doctors that "people are falling through time bringing every disease in history with them through your doors". Gwen gets a phone call from PC Andy and so she and Jack go to the cells. He has arrested a Roman soldier who fatally stabbed two people. The pair explain to him that the soldier was walking out from a nearby Roman fort and has fallen down a splinter in time into the present. Andy states that even if he believes them, he is still confused, not knowing how to treat the new prisoner, whether he has the same rights as a 21st century individual and how the CPS will cope with him. The pair solve this by drugging the soldier and taking him back to the cells at Torchwood.

Back at the hospital, Toshiko sees her mother who tells her in Japanese that the darkness is coming and that Toshiko must open the rift to stop it all. Her mother then vanishes.

At the prison, Gwen sees Bilis Manger in a cell. He apologises before disappearing. Back at the Hub, Ianto sees Lisa who tries to convince him to open the rift. Ianto does not believe that it is Lisa but being told to open the rift still makes him think. Owen and Jack fall out; Jack fires Owen, who goes to a bar to drown his sorrows. Diane appears and tells him to open the rift. He is tempted enough to do it...

Jack and Gwen go to Bilis' clock shop "A Stitch In Time". There they question him and Bilis reveals that he can step between eras in time "like walking into another room." He promptly demonstrates this when he disappears. Jack leaves, but Bilis returns and shows Gwen the future - Rhys has been killed in the flat with blood splattered everywhere. She runs to the flat to find Rhys alive. He won't come quietly to The Hub, so she shocks him and gets Jack to help her get him to Torchwood's base. Once there he wakes up and is very angry at Gwen. She says that she only wants to protect him. The team, minus Owen, are all in the central area of the Hub when the power goes off. Gwen runs to the cells, shouting Rhys' name.

The power goes off and Rhys' cell doors open. He tries to open the door, but Bilis appears and stabs him twice, twisting the dagger.

Gwen arrives and sees Rhys dead and no sign of Bilis. In the autopsy room, she cries and shouts at Jack, who consoles her. Owen then bursts in and tries to console her, but she shuns him. Owen then announces that he's opening the rift. Ianto follows him and Jack orders him to stop him, but Ianto says no. Toshiko and Gwen follow as well and begin to open the rift, however they are stopped by a security protocol that demands retina prints of all Torchwood personnel. Jack threatens Gwen with a gun, but she just walks up to him. He insults the gang by saying "Toshiko, the poor little girl who'll screw any alien that gives her a pendant, strong Owen who gets in a cage so that a weevil can maul him to death and Ianto Jones hiding a Cyberwoman in the basement." He then makes the mistake of doubting Gwen's love for Rhys because she slept with Owen. Gwen subsequently punches Jack, knocking the gun out of his hand. Owen seizes Jack's revolver and turns it on him. They're relieving Jack of command and "getting back what (they) love." Jack tells Owen that if he wants to take charge, he'd need "significantly bigger balls." Jack picks himself up and walks forward and Owen opens fire. Jack is dropped by a head shot but Owen fires another two rounds into his torso. Ianto, stunned, drops to Jack's side and implores Owen, "what have you done?" Owen answers he's "sick of people doubting" him as Gwen tries to calm him down.

With Owen calmed, the team activate the machine with all of their retinal scans, including Jack's. As the Rift opens, Jack revives himself. He comes round and asks what they've done and the team all evacuate the Hub as an earthquake splits across Cardiff. Outside, the team find Bilis, who speaks of a beast "cast out before time" named Abaddon trapped inside the Rift, before disappearing. Suddenly, a huge creature (similar to the Beast from Doctor Who's The Satan Pit) rises above Cardiff. Anyone in its shadow immediately dies, giving Jack an idea: he can't die, so Abaddon can feed off of his life. Gwen drives him to an open space and screaming, she tearfully tries to stop him without success. Jack shoves Gwen away, shouting at her to drive to safety, but still she doesn't leave, only stands crying by the SUV. Jack stands before Abaddon. The shadow begins to kill Jack, but a blue light flows out and begins to destroy Abaddon. The creature is dead and the rift is sealed. Jack lies dead before Gwen as she holds him, crying over his body.

The timeline has been restored with the opening of the rift. Rhys is alive. But at a cost — Jack has not re-animated. Owen, Ianto and Tosh appear resigned to the reality of his death but Gwen refuses to move from his side, telling them forcefully that she 'wants to sit with him'. Days pass, the team increasingly concerned for Gwen but she remains faithfully by Jack's side, watching him, occasionally smoothing down and re-arranging the body bag he lies in on the morgue slab. Ianto is seen crying into Jack's military coat. Finally, Gwen appears to give up. She picks up Jack's hand, pressing her cheek lovingly to the back of it before hesitantly leaning over him and kissing his lips. Gwen stands and walks away, almost crying from the morgue before hearing him gasp a breath and weakly calling, "Thank-you." Gwen sprints back to find him alive and smiling up at her.

Jack has regained some strength, although he is still pale, and Gwen accompanies him into the main Hub area, taking his hand and smiling up at him. Toshiko runs into his arms and Jack embraces her. Next, Ianto staggers forward, extending an unsteady hand but Jack takes him into his arms and kisses him. Owen, clearly shaken, then steps up to Jack as the Captain walks towards him. He begins to stutter his apology but Jack cuts him off. "I forgive you." Breaking down, Owen sobs into Jack’s shoulder and clings to him as Jack holds him comfortingly, stroking his hair.

The scene shifts to Jack's office, where Gwen and Jack are in conversation. Jacks tells her that although the rift is sealed, it will be more volatile than before. Gwen asks him what vision would have tempted him to open the rift. He says simply, "The right kind of Doctor." Jack walks out of his office to find the severed hand of the Doctor glowing, the preserving liquid bubbling actively, and its tank sounding some sort of alert. His excitement is obvious, a nervous smile mixed with confusion covering his face as a breeze sweeps through the area and the sound of the Doctor's TARDIS materialising is heard. Jack turns his head to something we can't see and smiles widely, and as the shot cuts to Gwen, the sound of the TARDIS dematerialising is heard.

Gwen enters the room, calling for Jack who is nowhere to be seen. The rest of the Torchwood team enter with coffee and Gwen asks them if they’ve seen Jack. Owen remarks that the Hub has been dishevelled after they had just cleared up. Gwen looks around the emptiness of the Hub, "He was just here." Crossing her arms over her chest, she frowns, "Something's taken him; Jack's gone."