Gwen is in bed with Rhys and watches him with a smile as he appears to sleep, but he tells her it’s rude to stare and she laughs. They start to kiss, then he gets up to make a cup of tea. Gwen’s phone rings and it’s Jack on the other end, calling to see if she’s watching the news. She joins Rhys in the front room and they watch a BBC News 24 report about a series of incidents around the world including footage of UFOs sighted over the Taj Mahal in India, men dressed in historical period costumes involved in a police shootout in London, the Beatles being spotted on the roof of Abbey Road studios, a guillotine appearing in Paris and a Samurai warrior on the rampage in the Tokyo subway system. Intelligence experts have apparently ruled out terrorist activity and are claiming it’s just a hoax, but religious groups believe these incidents vindicate their teachings about judgement day - this is the End of Days!

At the Torchwood Hub, Ianto reads out the relevant passages from various religious texts relating to the end of the world, including a reference to the demon Abbadon from the chapter of Revelation. Gwen thinks it all sounds a bit too close for comfort, especially when the injured Owen reports that some of their equipment is on the blink and they keep losing power. Jack has heard enough superstition and believes that people these days love anything that denies the randomness of existence. He’s been fielding calls all night from the Government, UNIT and the CIA. It appears that half the world is asking the same question - is this anything to do with Torchwood? He looks meaningfully at Ianto and Owen. Tosh has run a profile on every reported temporal anomaly and looked for a pattern. The group are shocked to discover that everything seems to originate from Cardiff, indicating that the cracks in time can be traced back to the Hub. These effects are caused by the ripples and aftershocks of the Rift splintering - and he directly accuses Owen of opening the Rift without knowing what he was doing. Owen points out that if it wasn’t for him, Jack and Tosh would still be in the 1940s, so they should stop complaining and do something about it. Jack orders them to collect everyone who’s fallen through time and bring them back here to their vaults, and they can decide what to do with them later. Owen realises that Jack can’t send these people back to their own time and they end up arguing. Jack assures them this is not the end of the world, but just then an alarm sounds and Ianto reports that a Priority 1 request has been put in for them to attend the local hospital. Mortality rates have gone through the roof and the authorities are sealing off the area and designating it as a ‘hot zone’. Owen and Tosh decide to go to the hospital and as soon as they’ve left Gwen rebukes Jack for picking on Owen so publicly. He reminds her that all their actions have consequences and he implies that she’s defending him because she still has feelings for him. Gwen’s phone rings again - it’s her old police colleague PC Andy asking for her help.

In the police cell, a Roman soldier hurls angry abuse at his captors while PC Andy, Jack and Gwen watch via the internal CCTV monitor. Andy explains that the man was arrested for brutally stabbing two men, but the police don’t know what to do as he doesn’t speak a word of English. Jack identifies the language as Latin and points out that the man isn’t dressed as a Roman soldier, he actually is a Roman soldier who was on his way to a Roman fort around 75 AD when time splintered and he ended up here. Andy doesn’t believe things like cracks in time occur in Cardiff, but Gwen confirms that it’s true. Andy needs to know what they’re meant to do with a prisoner from two thousand years ago. Does he have the same rights as anyone else? How’s this going to look to the CPS? Jack offers to take him off their hands, and he prepares an injection. They open the cell door for a moment and Jack slips in, then Andy asks Gwen whether she agrees with the word on the street - that this is the end of the world? She tries to laugh off his concerns, but he recognises her smile and has seen it many times before. It’s the smile she uses to reassure everyone when deep down she knows everything’s going to nuts.

The hospital has been converted into a massive isolation ward and all the staff are now going about their duties in full protective Hazmat suits. The doctor in charge shows Owen and Tosh to the body of the first person to die. The victim had no identification on her and she just appeared in the middle of A&E - no one saw her arrive and she didn’t register at reception. She started coughing up blood and was moved into isolation, but then an hour or so later the staff who treated her started showing similar symptoms - bite-like bumps, chills, headaches, fever and black patches on the skin, which indicates internal bleeding. It’s now starting to spread to other patients throughout the hospital. As soon as they realised the rate of infection they closed down the whole area, but there are already 30-40 other people affected. Owen examines the body, while Tosh looks at the women’s clothes and confirms that they’re not contemporary. Owen orders all the clothes and sheets for every patient to be burned immediately. He tells Tosh that the dead woman looks like she came from the 14th century and she’s infected Cardiff hospital with the Black Death! He realises it’s all his fault. He tells the doctor that they’re up against the plague and offers advice on the best course of medicine, but the doctor becomes angry. They’ve been told Torchwood will sort everything out and they’ve been waiting for them to help. Owen explains that people are dropping through time and they’re bringing with them every disease known throughout history. He storms out and Tosh tells the doctor to call them if things get worse, but he wonders how much worse can things possibly get..?

Tosh tries to catch up with Owen, but there’s no sign of him. However, she sees a figure standing at the end of the corridor and she stares in astonishment - it’s her dead mother! Her mother tells Tosh that something is coming out of the darkness and if there’s no other way, she’ll have to act. When Tosh asks what she’s supposed to do, her mother disappears and Tosh is alone in the corridor again. Owen arrives and tells her to hurry up.

Inside the police cell, Jack is using an alien device to scan the unconscious Roman soldier. Gwen suggests that if Owen opened up the Rift to bring him and Tosh back, they might be able to do the same to return all the displaced people. Jack thinks there’s a world of difference between opening the Rift and taking control of time. In any case, Owen has caused too much damage already and if they mess with it further, they could put the whole planet in danger. As she leaves, Gwen hears a whispered voice calling her name. She looks inside the next cell and see the caretaker Bilis Manger sitting there. She hears his voice inside her head telling her he’s sorry. Jack calls for her help and in the moment she’s distracted, Bilis disappears…

Back at the Hub, Jack and Gwen have placed the Roman soldier inside one of the cells. She’s told him what she saw and confirms that it was definitely Bilis, but Jack wonders what he has to be sorry for. Suddenly Ianto bursts into the cellar with a new prisoner - another Weevil. He tells them there’ve been thirty more reports of Weevils on the loose and they’re not going to be able to keep up at this rate. Everything seems to be on the increase. The Weevil starts whimpering, as if in pain, and Jack believes they must be time sensitive and the disturbances are getting too much for them. Ianto tells them the cells are full to capacity on all nine levels and he wonders whether he should activate the lower levels, warning that they’ve never been used in all the time he’s been here. Jack approves, then tells Gwen they should run a search on Bilis. They leave Ianto alone in the cell area - and then suddenly he sees his dead girlfriend Lisa standing at the end of the room, in her fully human form. He asks her why she’s here and she tells him there’s only one way to stop what’s happening before things get worse. She says thousands of people will die unless they open the Rift. Ianto closes his eyes in shock for a second - and in that moment Lisa disappears!

Owen and Tosh return and Jack asks how things were at the hospital. He tells him they’ve got an outbreak of the Black Death and Tosh, who appears to be still in shock from seeing her mother, adds that they’ve got the place under quarantine. The only consolation is that the plague is treatable these days, but what happens if the next carrier comes through with smallpox, Ebola or even something from the future that we don’t even know about yet? Owen becomes frustrated, complaining that all they seem to be doing is putting sticking plasters onto gaping wounds. He suggests Jack demonstrate better leadership and make some firm decisions about what they’re going to do. Gwen tries to calm him down, but Owen believes everyone else is thinking the same thing - Jack is the man with all the secrets so he ought to be able to tell them how to get out of this mess. Jack tells them there is no solution and he can’t fix it. This was never meant to happen and it’s all Owen’s fault. The first thing they all learned when they joined Torchwood is that they shouldn’t mess with the Rift, but he disobeyed those orders and everything that’s happened since is down to him. Tempers become frayed and Owen demands to know who Jack Harkness really is - he admits that they’ve done some searches and Jack doesn’t even exist, so why should they follow his orders? Jack relieves him of his duty on the spot and orders him to get out. The others try to protest, but Jack is adamant and tells Owen he doesn’t belong with them any more. He tells the others that if he can’t rely on their absolute trust, the same applies to them and if anyone agrees with Owen they should leave too. Owen realises nobody ever leaves Torchwood intact and that sometime in the next 24 hours, he’s going to be given the ret-con drug and all his memories will be erased. Gwen tells Jack things have gone far enough, but Jack won’t budge. Owen wishes them luck with the end of the world and leaves. Gwen is furious with Jack.

Later, Jack and Gwen head through the main Cardiff shopping centre to Bilis’s shop, ’A Stitch in Time’, which repairs and sells timepieces. They enter and browse around, realising that some of the clocks on display go back centuries. Jack theorises that Bilis scavenges antique timepieces from the past and brings them to the present to sell for a profit. Bilis Manger appears and greets them, and he and Jack recognise each other from 1941. Gwen asks him how he can be in two time zones at once and he explains that he can step across eras like walking into another room. At first it was the most incredible ‘gift’, but now he knows that it’s a curse because he can see the whole of history, yet he doesn’t belong anywhere within it. Jack’s return to this time had a price and time is splintering. This city exists on a Rift in time and the only way to make things right is to fully open it and let it suck back whatever came through. Jack refuses on the grounds that it’s too dangerous, but Bilis implies that if they don’t more people will fall through and lives will be lost. Jack pulls out a gun and points it straight at Bilis and demands that he come back with them, but Bilis apologises and then disappears. Jack calls for the group back at the base to trace for temporal activity around this location, then he leaves. Gwen hangs back for a moment - and then suddenly Bilis reappears and bars her way out of the shop. She asks him why he said he was sorry back at the police station, but he tells her it’s sometimes better to live in ignorance…but if she really wants to know, she can hold his hand and he’ll show her. Reluctantly she agrees and she suddenly sees a vision of Rhys dying on the floor in their house. He’s covered in blood and there are bloody hand-prints all over the walls. Gwen demands to know what Bilis has just shown her and he replies that it’s the future. She runs out of the shop in absolute terror and races past Jack, completely ignoring him. He chases after her, but loses sight of her.

Gwen returns home and races into the living room. She looks around desperately - and Rhys’s head pops up from behind the kitchen unit where he was bending down to clean the oven. For a moment she’s overjoyed, then she demands that they leave immediately and when he starts arguing, she takes out a stun gun and knocks him unconscious.

Owen is alone in a nearby bar when he hears his name being whispered. He turns round and sees a vision of Diane standing before him, but when he touches her she seems real. She tells him she’s lost and she begs him to bring her back. He’s not sure and says everything is out of synch, but she pleads with him to open the Rift. Moments later, she disappears and a tear rolls down Owen’s cheek.

Rhys wakes up with a start and finds himself locked inside one of the cells on the lower levels of the Hub. Gwen is watching him from outside. He thinks he must be dreaming, but she tells him this is where she works. She tells him she wanted to keep him safe but he becomes angry at the amount of nuts he’s had to take from her over the last few months. She asks him to trust her and although it may not seem like it at the moment, she’s just trying to take care of him. He hears the sound of the Weevils wailing in the next cell, but Gwen tells him to relax and says he’ll come back for him.

She returns to the main level and tells the others Rhys has woken up. Tosh brings up the CCTV image of him in the cell so Gwen can keep an eye on him. They don’t understand how Bilis was able to show her a fake vision, yet it felt so real. She becomes distressed at the memory of Rhys’s blood on her hands and Jack comes over to comfort her. He promises her it’s not going to happen and she trusts him. Suddenly all the lights in the Hub go out and there’s a complete power shutdown. Gwen panics and races back down to the cell area…

In the cells, the door to Rhys’s cell automatically opens by itself. He steps out and looks around, confused. He tries to open the main door to the corridor, but it’s locked. He d sees Bilis at the end of the corridor and assumes he works here, so he tries to explain that he’s Gwen’s boyfriend - but Bilis strides towards him and plunges a knife into his stomach! Then he steps forwards and stabs him again until Rhys collapses to the floor in a pool of his own blood. Before he passes out, Rhys sees Bilis go back to the other end of the corridor, then disappear. The power to the Hub restores itself, then Gwen and Jack burst into the cell area. They see Rhys on the floor, covered in blood, and Gwen becomes uncontrollably hysterical. She tells Jack they can bring him back to life, but he tells her there’s nothing they can do. She starts to scream…

Later, Rhys’s body is placed on the autopsy table. Gwen is in shock as Jack tries to clean up the blood on her hands. She realises she’s going to have to tell Rhys’s family, but Ianto offers to deal with that. Gwen realises he means they’ll cover it up the same way they did with the hospital porter when she first met them, so she refuses to let them ’deal’ with it. Although everyone is sorry about Rhys, Gwen is aware that they never even met him. This is what happens at Torchwood - they all end up alone. She again demands that Jack brings Rhys back and again he refuses. Ianto reminds her that they destroyed the resurrection glove, but she’s convinced there must be something else. If there’s something wrong with time, they can make everything go back to the moment before he died - otherwise, what’s the point of all this? She becomes hysterical again and attacks Jack and he holds her tight until she breaks down completely.

Just then Owen races in and immediately sees what’s happened. He tries to comfort Gwen, but she pushes him away. He asks Jack how many other people have got to suffer? Jack doesn’t answer so Owen declares that he’s going to finish this by opening the Rift. Ianto goes after him and Jack tells him to make sure he stops Owen - but both Ianto and Tosh declare that they’re going to help him! The Gwen runs after them, telling Jack that Bilis was right all along - he said if they open the Rift everything goes back to normal. The entire group is now working together on the Rift Manipulator, so Jack picks up a gun and goes after them…

Jack confronts the group and tells them to get away from the computer. He believes this is a trap set by Bilis and all the cracks around the world are just diversions. Gwen tries to access the computer, but she’s stumped by a security protocol until Ianto gives her the password he and Owen found earlier in Jack’s diary. Jack pulls out his gun and orders them away. He gives a final warning and the group turn to face him. One by one he reveals each of their weaknesses until he comes to Gwen - and when he reminds her that she was cheating on Rhys, she punches him so hard he falls to the floor and drops his gun. Owen retrieves it and declares that they’re relieving Jack of his command. Gwen returns to the computer, which tells her it needs the retina prints of all Torchwood personnel to proceed. Jack challenges Owen - so Owen shoots him dead…then fires bullet after bullet into his body. Everyone is stunned, then Gwen gently takes the gun from Owen’s hands.

Then one by one, the group register their retina patterns into the computer, including Jack’s dead body. Authorisation is complete and the computer asks them to confirm that they want to institute Emergency Protocol One, warning that its activation will endanger the entire infrastructure of the Torchwood base. Gwen is in doubt for a second, but when she sees Rhys’s body on the autopsy table, her mind is made up. She clicks ‘OK’ and an alarm immediately sounds out. The group are confused and afraid - then suddenly Jack revives and grabs Gwen’s leg, demanding to know what she’s done. Huge electrical arcs spark across the base of the water tower and then a fireball of blazing light races upwards, through to the top of the tower on the Cardiff Bay waterfront and then up into the sky.

The entire inside of the Torchwood base starts to shake, as if in the middle of an earthquake. The prisoners in the cells are overcome by the trauma and throw themselves against the cell walls - then they completely vanish! As Gwen and the others help Jack to his feet, there’s a series of explosions around the Hub and parts of the ceiling start to collapse. In the autopsy room, Rhys’s body disappears from the table. The group make their way to the main entrance, desperately trying to avoid the falling masonry around them…

Outside, the group help carry Jack into the street where cracks are already starting to form in the pavement. Gwen assures him everything will go back to normal, but the group comes to a sudden halt when they find Bilis standing before them. Gwen approaches him, a look of rage on her face, but Bilis announces that from out of the darkness “he” is come - the son of the Great Beast, cast out before time, chained in rock and imprisoned beneath the Rift. He hails Abbadon, the great devourer who has come to feast on life. The ground starts shaking and everyone follows Bilis’s gaze up into the sky…and they see the terrifying form of the horned demon himself, towering over them. Bilis predicts that the whole world will die beneath the creature’s shadow and they watch, helpless, as the gigantic monster rampages across the city. People in the streets scream in terror and run for their lives, but as the mighty beast’s shadow moves across them, they all die instantly and drop to the floor. Before long, the streets are littered with bodies. Bilis looks upon his god and knows that his work is done, then he vanishes.

Gwen asks Jack what she can do to stop it but he knows there’s only one way and he asks her to help him get to an empty space. She carries him to the SUV and they drive to nearby wasteland not far from the docks. He explains to Gwen that Abbadon is the bringer of death, but if it feeds on life what will it do if he offers himself up? They watch the giant creature in the distance, smashing its way through the buildings of the city and Gwen starts to panic for Jack. He pushes her away and orders her to drive away as fast as she can. He then stands in the middle of the wasteland and the creature senses his presence and changes direction, striding towards him. Within moments, the shadow of the beast passes over Jack and he screams in absolute agony, but although he falls to his knees, he doesn’t die. He continues screaming as his life essence is literally sucked from his body - but the energy is also having a noticeable effect on the demon. Cracks start to form in its skin and eventually it too falls to its knees, before finally dropping completely … Jack is dead. Gwen races over to him and cradles his body in her arms.

Later, Gwen rushes back to her flat and is both shocked and overjoyed to see Rhys standing there, confused. He doesn’t understand what’s happening as she was here with him just a moment earlier. She tells him to go to bed and get some sleep, then she’ll come back to him.

Later still, the group return to the Hub and prepare Jack’s body for storage. Gwen joins the others and Owen tells her he’s certain Jack is dead as his body is ice cold and there are no vital signs. Gwen reminds him that Jack survived earlier when he was shot and he told her when she first joined that he couldn’t die. She insists on sitting with his body, so Owen, Tosh and Ianto leave her alone with Jack. Hours pass, then days, with Gwen watching over Jack, patiently urging him to wake up. The others try to deal with the situation in their own way, and privately Ianto is particularly devastated, then Tosh goes to see Gwen and tells her she has to face up to the fact that Jack isn’t coming back. Reluctantly Gwen realises she has to let him go, so she holds his hand against her face for the last time, kisses him, then slowly walks away. At the last moment, she hears his voice whisper thanks to her - and she rushes over and sees him smiling back to her. Tosh and Ianto are shocked to see Gwen return to the main area, holding hands with the fully recovered Jack. Tosh hugs him, then Ianto goes over and they kiss passionately. Owen arrives, but is too shocked to know how to react. Eventually Jack tells Owen he forgives him, then holds his friend as he breaks down in tears.