Captain Jack Harkness is a man from the 51st century trapped in the past who leads the last remnants of the Torchwood Institute, a top secret British agency outside the government whose job it is to investigate alien goings on in the world, act in mankind's best interest, and, if needed, be the Earth's last line of defense.
WPC Gwen Cooper is at the scene of a brutal murder, when the "special ops," known only as Torchwood, arrive. After witnessing the group bring the dead man back to life, Gwen goes in pursuit of this mysterious organisation, only to see weirder things than she could ever imagine existed. Soon after, she begins to regret giving in to her curiosity, when she meets Captain Jack Harkness.
It's Gwen's first day on the job, and it's not going very well. After accidentally releasing a mysterious gas from a comet that landed, a new type of alien is let loose on the streets - an alien that's addicted to sex. Torchwood must find the inhabited body, and prevent anymore deaths from the violent form of sex.
Whilst chasing a man, Gwen retrieves an unusual machine that allows the user to see back into the past. It is considered dangerous, and no members of Torchwood are permitted to use it. But Owen has other plans, and witnesses a violent murder that took place over forty years ago. Using the information he gathered, Owen starts to track down the still-living murderer.
Ianto Jones hides a very big secret at Torchwood - his half-converted girlfriend from the Canary Wharf Battle - down in the basement. He is quick to hire a Japanese doctor who believes he can "cure" her. But things soon go wrong, and the Cyberwoman's destructive powers are released to the whole of Torchwood. Upgrading is compulsary.
Jack catches up with a very old friend of his, who is investigating fairy sightings in the local wood. After having visited her, Torchwood are informed of a man's mysterious death in a prison cell. Then, Tosh uncovers a series of localised, extreme weather patterns. Nobody at the organisation is sure of these events, or how they may be connected. Except Jack, who has witnessed the creatures causing this, almost a century ago.
Whilst investigating a group of unexplainable deaths in a village, the Torchwood team are separated. Discovering further, Jack, Gwen and Owen find a scared man, hiding from the thing responsible for the murders. But Tosh and Ianto go that one step extra, and locate the killer, who wants them as their next victims.
Tosh meets an unusual woman, Mary, at a bar, who gives her a strange pendant. She is upset, yet amazed by what she now has - the ability to read people's minds. However, Tosh finds this terrible curse, that contains her friends darkest secrets, must be broken. So she asks for help from Mary, the only person who knows, but first, Tosh has to get her into Torchwood.
Using the Resurrection Gauntlet that former Torchwood member Suzie Costello originally had, the team are able to bring a number of murder victims back to life. However, these all have a link with the now-deceased Suzie, and the group have no choice but to bring her back. After the process goes wrong, and permanently keeps her alive, Suzie manipulates the naïve Gwen into taking her to see her father.
Eugene Jones wakes up, finding himself lying on the middle of a road. He then discovers that he has been the victim of a hit-and-run incident, and is, now, not only dead, but invisible. Eugene recalls events leading up to his death, involving a mysterious alien eye. Simultaneously, Gwen investigates the suspicious circumstances around his fatality.
Three passengers from 1953 arrive in modern day Cardiff, when their plane flies through the Rift. With no means of travelling back, each person must adapt to their new life, starting personal relationships with the separate members of Torchwood.
Weevils are appearing all over the streets of Cardiff, and then disappearing again - but not by alien forces. People are abducting them, and using the Weevils for their own purposes, so Owen investigates.
Whilst investigating an old, derelict dance hall, Jack and Tosh are transported back to the 1940s, during the Blitz. Owen, Ianto, and Gwen realise, in modern day, that this has happened, and go in search of clues Tosh may have left. Meanwhile, back in the forties, Jack meets a very interesting man. One with the name Captain Jack Harkness...
With the Rift having been opened, people and objects throughout time are falling through it, and being spread across the world. "The thing in the darkness" has finally come, and Jack realises that he is the only one who can save planet Earth from the destruction that "the son of the Beast" will cause.