At her flat, Gwen watches Rhys sleep. He wakes up and they flirt briefly. When Rhys leaves the room, Jack calls to tell her to check the news. She turns on the television where a newscaster is reporting sightings across the world. There have been UFOs seen over India and Roundhead soldiers in London. Religious believers are insisting it's the End of Days.
At the Hub, Ianto is reading from the Bible and noting that it refers to the demon Abaddon. Tosh traces the pattern of events and determines that the Hub is at the center of it all. Jack informs Owen that he's responsible because he opened the Rift to bring Jack and Tosh back from the 1940s. Now they have to bring everyone that has fallen through the Rift to the Hub to lock them into the vaults. That's phase one, and Jack says he'll deal with phase two later. Owen demands a more specific answer but Jack admits he doesn't have any immediately ideas. However, he insists that it's not the end of the world.
The team gets an alert from the hospital that mortality rates are climbing. Owen says he'll go on his own but Jack insists on sending Tosh with him. Once they're gone, Gwen attacks Jack for picking on Owen, warning that they all have feelings. He responds by saying that she would know, alluding to her affair with Owen. She points out that Owen saved him. Before they can pursue the matter, PC Andy calls Gwen to tell her they have a Roman soldier in Holding that killed two civilians. Gwen and Jack go to the station and take the soldier off of Andy's hands. As Jack deals with the soldier, Andy wonders if it's the end of the world and isn't convinced by Gwen's reassurances.
At the hospital, Gwen and Tosh meet with a doctor who informs them that the woman appeared out of nowhere, started dying, and spread her disease to others. They realize the woman has fallen through the Rift from the 14th century and she has the Black Death. Owen realizes that it's all his fault. He prescribes an antidote but the doctor wonders what Torchwood is going to do something. Owen tells him what's going on and warns him he'd better be ready. When the doctor worries how much worse things can get, Gwen doesn't answer. Owen storms off and as Tosh goes after him, she sees her dead mother in the hallway. Her mother says that the "darkness" is coming and Tosh will have to do it if no one else can. When Tosh tries to figure out what she means, her mother disappears.
At the jail, Gwen wonders if they can use the Rift Manipulator to send the displaced persons back. Jack warns that it's too dangerous and insists that he's never let Gwen down. Gwen walks away and comes face-to-face with Bilis Manger, who is sitting in a cell and telepathically says he's sorry. Jack interrupts her and Bilis disappears. They go back to the Hub and Gwen tells Jack what she saw. Ianto brings in a newly captured Weevil and Jack speculates that they're time-sensitive. The cells are now filled with Weevils and they're out of run. Jack and Gwen leave to run a search on Bilis. As they leave, Ianto's dead girlfriend Lisa appears to him. She tells him that thousands of people will die unless he opens the Rift. She disappears and Ianto finds himself alone with the Weevils.
Owen and a distracted Tosh return to give Jack their report. Owen warns that while they have the outbreak under control, any number of other diseases from the past or future could come through. He insists they need to prepare and come up with a plan. Owen tells Jack to lead them and give them instructions, and tell us a few of his secrets. Jack tells them that there is no solution and he can't fix it: it was never meant to happen. Owen wonders if he should have bothered bringing him back, and wonders why they should follow Jack's orders when he has no background or history. Jack relieves him of duty and tells him to get out. Gwen insists they need to work together but Jack tells them all that he needs their complete trust or they have to go. Owen realizes he'll have his memories erased within 24 hours and bids them all a final goodbye before leaving.
Jack and Gwen go to Bilis' timepiece shop, A Stitch in Time. Jack realizes that Bilis scavenges antique clocks from other eras and sells them for money in the present. Bilis comes in and casually admits that he can easily step across eras. He once believed it was a gift but now considers it a curse: he can see the whole of history but doesn't belong anywhere. Bilis explains the only way to make things right is to fully open the Rift and let everything else fall back. Jack warns that it's too dangerous and Gwen wonders if they can eve do it, but Bilis says that they can. Jack draws his gun and insists that Bilis comes back with them, but he disappears into time. Jack orders a temporal trace and leaves. Gwen hangs back for a moment and Bilis returns. He insists that he's not her enemy and offers to show her what she needs to know. He takes her hands and shows her a vision of the future where Rhys is killed. He apologizes again as she runs out past Jack and goes to her flat. She enters and discovers that Rhys is unharmed. Gwen insists they got to go and when he hesitates, she stuns him with a taser.
Owen is at a bar when he hears Diane whisper to him. He turns and finds her next to him. She insists that she's lost and needs him to bring her back. When Owen says he doesn't know how, she tells him to open the rift. Diane disappears and Owen draws a deep breath.
Gwen takes Rhys to the Hub and locks him in a cell. She tries to reassure him but has no choice but to leave him locked up for his own safety. She rejoins the others and has Tosh leave the CCTV in the vaults tuned to Rhys. Gwen insists that the vision she saw was total real and she could feel the blood on her hands. Jack assures her Rhys isn't going to die and gets them back to work. The power fluctuates and they realize they have a security breech. Gwen runs to the cells.
In the cell area, the doors open and Rhys steps out and goes to the exit door. It's locked and Rhys sees Bilis at the other end of the hallway. Bilis stabs him in the stomach twice and leaves him to die before teleporting away. Gwen and Jack come in a few seconds later and find him dead. Gwen embraces him, crying. They take him to the morgue and Jack cleans the blood from Gwen's hands. She insists on telling Rhys' family but then tells Jack to bring Rhys back. He says they can't and Gwen attacks him, insisting there's no point to Torchwood if they can't help. She collapses, sobbing, into Jack's arms.
Owen returns and tries to hold the grieving Gwen, but she tells him not to touch her. He asks Jack how many others have to suffer and insists on opening the Rift. Ianto, Tosh, and Gwen go after him, saying they plan to help so they can restore their loved ones. Jack grabs a gun and goes after him, and orders them away from the computer. He explains that the entire thing is a trap and Bilis wants them to open the Rift. When they refuse, Jack aims his gun and points out all the flaws, and that Gwen has been sleeping with Owen. Gwen punches him and Gwen grabs the gun. They realize that the security protocols require the retinal scans of all Torchwood members. Owen shoots Jack three times as the others stare in shock.
The four members use the retina scanner to activate the emergency protocol. The computers warn that the procedure could endanger the Hub. They hesitate for a moment and Gwen looks at Rhys' dead body, and then begins the procedure. As the alarms go off, Jack comes back to life and demands to know what they've done. Power shoot up through the central core and out into the sky while the prisoners go berserk and the Roman soldier disappears. Rhys' corpse vanishes as windows shatter and the walls start to come down.
Everyone gets outside only to find Bilis waiting for them. He tells them that the Son of the Great Beast, imprisoned beneath the rift, is finally freed. A gigantic demon steps fourth and walks across Cardiff as people run in terror. As his shadow passes over them, they die by the hundreds.
As Bilis announces that his work is done, Gwen and the others look about at the devastation. They ask Jack what to do and he tells them to get him to an open space. They drive out to a field and Jack figures that if Abaddon feeds on his life, then his eternal life should overload it. Jack dares the Great Beast to come for him and he dies in his shadow… again and again. His life force flows into Abaddon and it collapses dead. Gwen runs to Jack's side and cries over him as he lies dead for the final time
Later, Gwen goes back to her flat and discovers that Rhys is alive with no memory of what happened as time has reset. She tells him to go to bed and she'll be back for him. She goes back to the Hub where the others have confirmed that Jack has no vital signs and isn't resurrecting. before they put him in a drawer, Gwen asks to sit with him for a while. The others leave and Gwen tells Jack to wake up. He doesn't and she waits throughout the night. The others wonder how long she'll wait until she accepts Jack's final death. Days go by and Tosh tells Gwen to let him go. Gwen finally takes Jack's hand and kisses him goodbye and then walks away. As she does, she hears Jack say "thank you." She goes back as Jack looks up, smiling.
Jack goes to see the others. Tosh embraces him and Ianto shares a brief kiss. When Owen comes over, he tries to stutter out an apology and Jack forgives him as they embrace. Jack confirms that the Rift closed when Abaddon was destroyed, but it'll be more volatile than ever. She wonders what vision of a loved one he saw, but he admits he saw nothing. When she wonders what might have tempted, he only notes "the right kind of doctor." As Jack goes to see where the others are with the coffee, he sees the severed hand glow in its jaw. Smiling, a breeze stirs up and he hears a strange noise that he recognizes. Gwen goes out to discover that Jack has disappeared. The others return and realize that Jack is gone.