20 November 1953: A Swedish cargo ship, the Facklaträfat, arrives in Cardiff after midnight, with a crate that the Russians must not be allowed to get their hands on. Four dockworkers -- Frank, Wilf, Hassan, and Michael -- have been paid overtime to receive the ship's cargo, but as the crate is lowered to the docks, it begins to hum and then explodes. Two men named Cromwell and Valentine, who have been watching from the shadows, rush to the scene of the explosion to find that the 24-year-old Michael has been blasted halfway across the dock and that the other three workers have been killed. All that's left of the crate is a fragment with the word "Torchwood" stamped on it.
2008: It's a quiet day at the Hub; Jack has cleaned the SUV, Tosh is tracing an electromagnetic pulse from the Vaults, Ianto is watching James Bond movies, and Owen is watching Janet the Weevil as she paws at the wall of her cell every 26 minutes. Gwen has had an argument with Rhys, but as it's so quiet, Jack orders her to go home and make it up with him. Before she can go, however, the Hub's intruder alarms go off, the pulse that Tosh had detected ramps up in intensity, and the CCTV reveals that a humanoid figure has just appeared in the Vaults. Jack investigates, and is horrified to recognise the man as Michael Bellini, the dockworker from the 1950s. While Owen examines the confused and frightened Michael, Jack retreats to his office, haunted by memories and unwilling to tell the others how he first met Michael. Gwen manages to calm Michael down, and he tells her about the explosion in 1953...
1953: Cromwell and Valentine visit Michael in hospital, but he's unnerved by their strange questions and upset to learn that his friends are dead. He visits his sister Maria after he's released from hospital, but her loutish husband Rhodri doesn't care what Michael is going through. Michael goes to the Ship and Pilot pub in Butetown, but meets Pete's son Frank, who wants answers about his father's death that Michael is unable to provide. Upset, Michael leaves the pub, only to see Cromwell and Valentine watching him from across the street. Terrified and confused, he starts to run -- and is suddenly transported to 2 January 1941, to his own street in the middle of the Blitz. Confused, he sees his younger self leaving his house with his mother and sister, and sees his mother turn back to the house as if to fetch something. The older Michael rushes forward, shouting out a warning, but a bomb hits the street, destroys Michael's old house and kills his mother. A grey-skinned man in a suit and bowler hat walks towards through the wreckage, looking directly at the horrified Michael and calling him the Traveller...
2008: After examining Michael, Owen realises that he's seen the young man before on one of his first days on duty as a doctor. Michael had been brought into hospital looking as if he'd been caught in an explosion, but when he claimed to have travelled between the years 1941 and 1953, Owen recommended to his superior, Dr Balasubramanian, that Michael be given a psych evaluation and then sent to St Helen's Hospital. The same day, he saw a young boy named Darren Lucas who had been hit by a car; later that day, Darren died of a blood clot that the initial examination had missed, and the guilt-ridden Owen forgot all about Michael until today. When Owen tells his story, Tosh remembers that she's also met Michael before -- and after she's told her story, Gwen reveals that she has as well.
The early 1980s: Toshiko is five years old, and her father has returned to Osaka for the Tenjin Festival. That night, Tosh's mother tells her a fairy tale about a rich man named Sentaro, who sought immortality from Jofuku, patron god of the hermits of Mount Fuji. Jofuku sent Sentaro to the Land of Perpetual Life, but eternal life proved unfulfilling -- and Sentaro learned that from here, he would never reach the Land of Horaizan, the paradise beyond the gates of death. Sentaro begged Jofuku to return him home, but he encountered a storm on the way back, fell into the ocean, and was menaced by a shark. He then awoke in Jofuku's shrine, and realised that he had been granted a vision teaching him to be content with his life and with the fact that he would one day die.
Toshiko goes to sleep happy. The next day, her parents leave for work, her grandmother falls asleep while watching television, and Toshiko finds a strange man hiding in her closet. He tells her that his name is Michael, and seems confused and frightened to learn that he's in Japan. The young girl offers to fetch him some food, but a grey-skinned monster in a suit and bowler hat materialises in the kitchen and attacks her, demanding to know where the Traveller is. Michael rushes forward to defend Toshiko and vanishes into thin air, and the grey man vanishes as well, telling the terrified child that they will meet again.
A few years ago: Gwen Cooper meets her new partner, PC Andy Davidson. She's having an off day, and thus lets Andy deal with a young shoplifter and with the man who runs into their police car, babbling that he's just seen a monster attack a young girl in Japan. Michael claims to recognise Gwen from the "underground place," but Andy manages to calm him down, and he and Gwen take Michael to the station for a psych evaluation. Gwen thinks no more of the incident until Michael turns up in Torchwood...
2008: Tosh deduces that Torchwood is likely to have stored whatever exploded on the docks and caused Michael to become unstuck in time, and she and Owen track down the artefact in the Vaults. It's a mysterious sphere that was shipped back from a British polar expedition, and it appears partly melted. Meanwhile, Ianto and Gwen determine that the men Michael met in 1953 were Kenneth James Valentine and Charles Arthur Cromwell; Valentine, a former policeman, vanishes from official records in 1947, and Cromwell was a former Torchwood employee who died in 2006. When Ianto sees Cromwell's photograph, he recognises him from a very brief meeting in 2006; Cromwell arrived at Torchwood One to question a Welshman who had appeared out of nowhere in the building, and shortly afterwards, the building was evacuated briefly for reasons that were never explained to Ianto.
Jack emerges from his office and identifies the partly melted sphere as a Vondraxian Orb. The Vondrax are an ancient race that feed off the tachyon energy created when quantum probabilities collapse into alternative timelines, and the Orb is a storehouse of such energy. The Vondrax can ride tachyon waves through Time, using the Orbs to change history and create more alternative timelines so they can feed. Torchwood tried to get its hands on this Orb before the Russians could, but apparently the tachyon energy interacted with the Rift and caused the Orb to explode. Michael was irradiated with the tachyon energy and has been leaping uncontrollably back and forth through Time ever since. The Orb has been stored in the Hub since 1953, emitting low levels of tachyon energy; the current team members have all absorbed trace amounts of that energy into themselves, which is why Michael has been leaping back into their pasts.
The past: Gwen and Andy deliver Michael to the police station, where he is given a psych assessment and sent to hospital. The monsters in bowler hats appear in the ward, and Michael panics and leaps again, this time to Loading Bay 5 of Torchwood One in London. He is immediately captured and placed in solitary confinement in Information Retrieval, where he is interrogated briefly by Ianto Jones' immediate supervisor, Bev Stanley. When Michael identifies himself, Stanley sends for Cromwell, who meets Ianto briefly on his way in; however, Cromwell already knows what's going to happen to him. Michael doesn't understand when Cromwell refers to something called the Hamilton's Sugar incident from 1967, but Cromwell nevertheless warns Michael that the creatures stalking him are called the Vondrax; they don't like mirrors, and they won't stop coming for Michael until he's dead. The Vondrax then attack Torchwood One, killing everyone in their path as they close in on Michael. Michael leaps to safety as the Vondrax break into the interrogation room, and Cromwell, who already knew what was going to happen to him, waits peacefully for them to kill him. Ianto evacuates safely from the building along with his close friend Lisa, but he never finds out what caused the evacuation, and he never sees Bev Stanley again.
2008: Gwen calls Rhys to apologise that she won't be home for dinner again. Owen looks up Michael Bellini in Torchwood's records, but can't find much, except for a brief mention of something called the Hamilton Sugar incident. Tosh studies the alien Orb, trying to unpick its secrets -- and glimpses a man in a bowler hat, down in the Vaults on the CCTV cameras. Jack visits Michael in the boardroom, but leaves again, unable to tell the innocent young man what Jack knows will soon happen to him. Ianto finds Jack watching Michael on the CCTV, and realises that Jack knows more than he's saying -- and that he really doesn't want to talk about it.
1967: Somebody in London has been asking questions about Jack Harkness, and he tries to set a trap for his stalker by offering a rare Shakespearian manuscript for sale. This apparently gets the attention of Hugo Faulkner, a rich young man who owns a restaurant near Carnaby Street -- but when Jack meets with him, Hugo reveals that he knows that Jack is the time-traveller who stole the manuscript from Thomas Sheridan in 1765. Jack realises that he's the one who's walked into a trap, but escapes from it by being more willing to drive his car over Hugo's associates than they'd expected. As Jack returns to Cardiff, however, a stranger named Michael Bellini suddenly materialises in his car and tells the surprised Jack that they've met in the future. Jack stops Michael from saying more, but decides that the young man can be trusted. Michael hasn't eaten properly for days, and Jack thus takes him out to dinner -- but as they eat, Jack sees Hugo Faulkner watching them from across the street.
Jack takes Michael back to his sister Maria's house, hoping to put him safely out of the way while Jack deals with Hugo; however, Maria doesn't believe that the young man standing before her is the brother who disappeared 14 years ago, and threatens to call the police. Jack takes the upset Michael out to a pub, and, realising that its clientele is mostly gay, Hugo admits that he had feelings for one of his fellow dockworkers but never admitted it to them. He can tell that Jack is lonely underneath his confident exterior, and tells Jack that in the future, he will have friends. Jack rents a room for Michael at the Shangri-La hotel, and Michael invites Jack to spend the night with him. Afterwards, he admits to Jack that this was his first time.
The next day, Jack and Michael visit the Cardiff Museum to meet an old man named Sam who has the gift of precognition. Sam tells Jack that Hugo is a dangerous fool, but that Jack will meet with him anyway to get answers. Michael insists upon accompanying Jack to the meeting, hoping for some answers of his own. Hugo is waiting for them at a funfair, and he takes them to the abandoned Empire Pavilion to meet his associates, a group of young beatniks who have collected evidence that the government is suppressing the truth about alien life. The beatniks believe that nuclear holocaust was averted by the spies who leaked information on the Bomb to Russia, thus ensuring that the world's two superpowers could keep watch on each other. To ensure a similar parity in the extra-terrestrial arms race, Hugo's group intends to turn Jack over to the Russians. Russian soldiers led by the coldly beautiful Tatiana Rogozhin emerge from hiding, take Jack and Michael into custody -- and then kill the naive Hugo and his beatnik associates before marching their prisoners away. Their destination is a secret substation for the Russian Committee for Extraterrestrial Research, KVI -- and Michael is horrified to see that it's hidden in an old warehouse that used to belong to Hamilton's Sugar.
Jack and Michael are separated, and Michael is interrogated by a familiar figure: Kenneth Valentine, who switched sides and now works for the Russians. Valentine tells Michael that orbs such as the one that exploded at the docks have appeared throughout human history, and that every time one has surfaced, shape-shifting monsters have tracked it down, killing everyone in their path. Michael's body absorbed all of the energy from this orb when it exploded, and the creatures are following him through time to recover it. The Russians intend to take Michael to Moscow, where their scientists will attempt to analyse and extract the powerful energy from his body before the creatures track him down. Jack is tortured for information on Torchwood, but provokes his torturer, Yevgeny, into killing him. Tatiana and Yevgeny conclude that the stories about Jack's immortality were false, and Tatiana leaves Yevgeny to burn Jack's body. However, Jack revives while Yevgeny's back is turned, and he overpowers Yevgeny and his other guards, tracks down Michael, knocks Tatiana unconscious and shoots Valentine dead.
Before Jack and Michael can escape, however, the figures in bowler hats arrive and begin slaughtering their way through the Russians to get to Michael. Jack and Michael are finally able to get a close look at the Vondrax, and realise that they've taken a familiar shape and twisted it just enough to make it look terrifying. Jack tries to hold off the Vondrax while Michael flees to the roof, and when the aliens get close to him they collapse and wither away, thick black ichor bleeding out of their noses and mouths. However, Michael now knows why the creatures are following him, that they'll kill anyone who gets in their way, and that they won't stop coming until he's dead. He tells Jack that he's sure, and Jack takes Michael in his arms as Michael jumps off the roof of the warehouse. They are holding each other as they hit the water nine storeys below, and they die in each other's arms. Later, Cromwell arrives with a cleanup team, intending to suppress the humiliating fact that a secret KVI substation had been set up so close to Torchwood Three without their knowing. Jack climbs up out of the water alone, and walks off without a word when Cromwell asks him what happened.
2008: Jack tells Ianto everything, and Ianto compassionately tells him to go be with Michael while he still can. Jack tells Gwen that the Vondrax don't like mirrors, and then takes Michael up to Roald Dahl Plass to see how the city has changed in the past forty years. Moments after they've gone, the Vondrax attack the Hub, see Jack and Michael on the CCTV, and ascend to the plaza. When they draw near to Jack, however, they shudder and die, unable to cope with the darkness inside Jack's head. The terrified Michael then vanishes, and although Jack knows what will happen to Michael next, he can do nothing about it. He thus descends back into the Hub, where the others have huddled around the water tower. Repulsed by their own reflections, the Vondrax are unable to get close enough to kill them, and again, Jack's mere presence is enough to kill the Vondrax when he arrives. Once they've gone, he tells his team that it's over, but Owen points out that they were nearly killed by something from Jack's past and just how many skeletons he has in his closet.
As Jack had promised, the incident is over, as Michael's future already occurred in 1967. Ianto returns to his James Bond marathon, and Gwen returns home to Rhys and apologises for their silly argument. Tosh returns home to look through old photographs and remember the good times with her family. Owen just returns home, walking past the clubs where he once would have been drinking and picking up women. Jack takes the melted remains of the Vondraxian Orb -- now empty and lifeless, as the last of the trace energy was absorbed into Michael's body while he was here -- and throws it into the water near what was once the Hamilton's Sugar warehouse. He then walks away, and doesn't look back.