Over the course of two days, all the children in the world stop in their tracks, and speak, in unison and in English, "we are coming". Home Office Permanent Secretary John Frobisher is aware these events are tied to an alien race known as the 456, due to the wavelength they communicate on. The 456 appeared in 1965, secretly communicating with the British government and offering a cure to a new strain of Indonesian flu destined to wipe out 25 million, in exchange for 12 children. Captain Jack Harkness was one of four soldiers that was part of the operation to give the children to the 456s. As public knowledge of the exchange would be disastrous for the British government, Frobisher orders, through troops under Agent Johnson's command, the assassination of those involved in the previous contact. Johnson plants a bomb in Jack's stomach, which goes off inside of the Torchwood Hub in Cardiff and destroys it. Aware of Jack's regenerative abilities, Johnson's troops collect Jack's remains and lock them in a secure facility, monitoring the reforming of his body. Gwen Cooper, her husband Rhys and Ianto Jones, due to their association with Jack, become fugitives from the law. Frobisher also orders construction of an isolation tank inside the Thames House to receive the 456s when they arrive.

The remaining Torchwood team make contact with Lois Habiba, a new personal assistant in Frobisher's office who has seen his classified files. Lois helps the others to locate and rescue Jack; they, in turn, provide her with a special Torchwood contact lens that will allow them to see what she sees, hoping she will help them learn the cause of these events. Torchwood also has identified and rescued Clement McDonald, originally one of the twelve children to be taken away but left behind by the 456. Clement has since become senile, but still responds in the same way as the rest of the children to the new 456 signal.

On the third day, the 456s arrive on a column of fire over the Thames House before appearing in the isolation tank. They demand that 10% of the world's population of children be handed over to them and threaten to destroy the human race if their demands are not complied with. Torchwood and Lois announce their continued presence and intervene under threat of revealing the 456s' threat to the world. Jack and Ianto approach the 456s and demand that they leave. The 456s trigger a lockdown of Thames House and inject it with a lethal gas, killing inside, including Jack and Ianto. At the same time, they send an auditory signal to Clement, killing him. When Jack revives, he and Gwen mourn over their loss.

With Torchwood's failure, and Lois in prison for charges of treason, the governments of the world silently make plans to deliver the children as promised; Prime Minister Brian Green decides to cover up their country's actions as inoculation shots while at school. The 456 reveal they need the children as their bodies emit a chemical that acts as a recreational drug to them. Frobisher discovers his children are part of those that have been selected, and quietly kills his family and then himself. As parents have kept children at home from school, Green orders military measures to secure the remaining children. While Gwen and Rhys help to protect Ianto's sister Rhiannon's daughter and several other local children from capture, Jack and Johnson consider a means of stopping the 456s. They realize that they audio signal used to kill Clement could be used against the 456s. However, it requires that one child act as the focal point for the transmission, likely killing him or her. Jack is left with no choice but to use his daughter Alice's son, Steven, who is the closest child available. Jack and Johnson successfully send the signal, amplified through all the other children, and the 456s suffer in pain before withdrawing from the earth. Steven dies and Alice becomes furious with Jack.

The world recovers from the events. Green suggests that they simply cover it up and place the blame on the United States, but Bridget Spears, Frobisher's direct assistant and Lois' superior, reveals that she is wearing the contact lens that Lois used and has recorded this conversation and will release it, putting an end to Green's political career. Six months after the events, Gwen and Rhys meet with Jack, who had been traveling the world on his own, trying to rid himself of the guilt. Jack states he needs to make a new life for himself and plans to travel into the stars. Gwen brings Jack his vortex manipulator, found in the wreckage of Torchwood, as a departing gift as he teleports away.

Nine months later, Gwen started up Torchwood again and hiring a new team.

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