An alien race known as the "456" demand 10% of the Earth's children to be handed over. The chemicals within Earth children brings pleasure to the 456, and the children going to hooked up to them as recreational drugs to make them "feel good". Consequently Torchwood team are forced to fight against the British government and their attempts to concede to the aliens' demands, to prevent any of Earth's children from being handed over.

The bomb explodes, blowing up Torchwood. Gwen escapes and goes on the run with husband Rhys, with an army detachment under tough female Captain Johnson in pursuit. Dekker gives Frobisher cryptic written plans for a mysterious edifice the aliens - the 456 - want building though not even the P.M. knows what it is. Lois, Frobisher's new temp, accidentally finds secret information on Torchwood in her computer and is curious but Frobisher tells her Jack was the terrorist who caused the explosion.Gwen and Rhys hide in a lorry bound for London, where she discloses her pregnancy. She is keen to get an explanation from Frobisher,unaware that he is out to kill her. Ianto escapes separately, seeking help from his sister, whom he meets in a park where children chant "We are coming. Tomorrow." Clem, on the streets, takes up the chant. Lois, now mistrustful of her boss, takes a call from Gwen and Rhys, meeting them secretly to tip them off that they are in danger. They infiltrate a 'funeral',saving Jack, whose body has regenerated, and are in turn rescued by Ianto. Frobisher and Dekker, having obeyed instructions, await the aliens.

The team hide out in a former Torchwood holding facility, stealing to survive. Gwen meets with Lois, giving her a laptop and special contact lenses to report back to her. Gwen also has Clem, arrested for an affray, released and safe with the team. Ms. Johnson locates and captures Alice and her son after Alice has tried to ring Jack, soon after which children state that 'We' have arrived and a pillar of fire turns into green ooze as the alien leader communes with Frobisher, watched by the Torchwood team,thanks to Lois. Everything is bound up with the events of 1965,as the alien voice tells Frobisher and Jack also comes to realize. The aliens want ten per cent of the world's children to go with them whilst Clem recalls Jack as one who allowed the alien abduction in Scotland, which Jack cannot deny.

Jack is forced to confess how he helped broker a deal in 1965 when the 456 aliens offered an antidote against a deadly universal flu virus in exchange for twelve children who would 'live forever.' Clem and the team watch via Lois's laptop as the aliens tell Frobisher they will 'wipe out the human species' if their request is not met, and a camera reveals the apparently zombic Scots victims, said by the aliens to be unharmed. Frobisher rejects Jack's offer of help in return for Alice and her son's release. He attends a Cabinet meeting which agrees that the Cabinet's children will be spared and that lower-class kids should be sacrificed instead.This is recorded by Lois and sent to safety with Rhys,giving Ianto and Jack leverage to talk to the aliens but the latter's' response is to unleash a virus which kills dozens, including Clem and,seemingly,Ianto. The government feels forced to capitulate.

With little choice now but to give in to their demands, the British authorities begin to round up the children under the pretense of giving them inoculations. Panic begins to set in as parents begin to wonder what is happening to their children. Captain Jack is released as are his daughter and grandson and he tries to find a way fight the 456. Gwen and her husband return home to tell Ianto's sister what has happened but they arrive to find a house full of children, whom they try to save from the arriving soldiers. With Fobisher no longer available, Col. Oduya becomes the intermediary and the 456 reveal the reason they need the children. For Captain Jack his finding a way to fight the 456 forces him to make an incredible sacrifice.