Summary
Day One
Children of Earth begins with children coming to a complete stop at exactly the same time across the world. Torchwood investigates as the children begin to chant a message "we are coming", and discover one adult chanting along with the children, identified as Clement McDonald (Paul Copley), who evaded abduction by the aliens — known to the British Government as the 456 — in 1965. He has a heightened sense of smell, and through this ability reveals that Gwen (Eve Myles) is three weeks pregnant. Jack (John Barrowman) and Ianto (Gareth David-Lloyd) attempt to find children to study, but Jack's estranged daughter Alice (Lucy Cohu) refuses him access to his grandson Steven (Bear McCausland), while Ianto's sister Rhiannon (Katy Wix) stops him from taking his niece. The Prime Minister Brian Green (Nicholas Farrell) foists responsibility for the situation onto Home Office Permanent Secretary John Frobisher (Peter Capaldi). Frobisher orders the murder of Jack and other persons who were involved in the events of 1965. Jack is killed by doctor Rupesh Patanjali (Rik Makarem), whom he had considered hiring as Torchwood's new medical officer. Before he resurrects, Government agent Johnson (Liz May Brice) has a bomb placed in his stomach. The bomb later detonates, destroying the Torchwood Hub and killing Jack once more.
Day Two
Gwen flees from Cardiff Bay and travels to London with her husband, Rhys (Kai Owen). They attempt to contact Frobisher, but are met instead by Lois Habiba (Cush Jumbo), a new personal assistant at the Home Office, who gives them information on Jack's location. Agent Johnson has taken what is left of his body to a secret governmental prison, where he regenerates. His cell is then filled with concrete to prevent his escape. Jack is rescued by Ianto, who breaks out the concrete block using a forklift truck. He drops the block into a quarry, shattering it and releasing Jack.
Day Three
The 456 arrive in Britain, at Thames House and are unofficially met by Frobisher, who requests that the previous contact between the 456 and the UK not be discussed in further meetings due to the possible embarrassment the revelations would entail. Soon afterwards, UNIT and the Prime Minster agree that Frobisher should be the sole contact with the 456. While preparing for his first official meeting with the aliens, Frobisher is called by Jack, who demands to meet with the 456 under threat of making public the events of 1965. Frobisher tells him that Jack's daughter and grandson are being held hostage and will be killed should he act. He then begins diplomatic talks with the 456, with Torchwood watching by way of contact lenses containing hidden cameras, which Gwen persuaded Lois to wear. The 456 demand a gift: 10% of Earth's children. Clement, who has been collected by Gwen and brought to the team's temporary base, recognises Jack as the man who, in 1965, gave twelve children to the 456.
Day Four
It is revealed that Jack gave away the children in exchange for a cure for a new strain of Indonesian flu, which the 456 claimed would kill 25 million people. Meanwhile, the government tries to bargain with the aliens, but the 456 threaten the human race with annihilation if their demand is not met in full. Prime Minister Green and his cabinet then decide that the government will offer the 456 those 10% of children whose schools have been placed in the bottom of the British league of school achievement. At this, Lois confronts the cabinet with a message from Torchwood, announcing that Torchwood has recorded their discussions and will make the information public unless Jack is allowed to meet with the 456. Agent Johnson tracks down Gwen with the help of The Operative (Ben Loyd Holmes). Instead of killing Gwen, as she originally set out to, Johnson listens to what Gwen has to say about the people in charge, and sits watching what's going on with the Torchwood operative. The 456 then kill Clement by generating a burst of sound, which causes him to die of cerebral hemorrhaging. Granted access, Jack and Ianto tell the 456 they will not sacrifice a single child. In response the 456 declare war and release a virus into the building which kills almost everyone inside. Ianto succumbs to the virus and dies in Jack's arms, just before Jack himself dies.
Day Five
Green orders Frobisher to continue with the plan. Questioned why they want the Earth‘s children, the 456 reveal that certain chemicals produced in their bodies act as a kind of recreational drug for them. To gather the children, Green informs the country that some children will receive an inoculation against the effects of the 456, when in actuality these selected children will be given to the aliens. Despite official agreement that children of the political elite will be spared, Green tells Frobisher that his daughters will be taken, to convince the public that the government were victims also. A desperate Frobisher then kills his family and himself. The army are dispatched to collect the selected children, but the public start to fight back in defence of their children. In Cardiff, Gwen and Rhys help Ianto's family hide the children they are looking after. While hiding, Gwen records on a camera a message explaining "how the world ended": in it, she comments she now understands why the Doctor, the person Jack venerates so highly, doesn't always return to save the day, because at times like the present he is too ashamed of humanity. Jack realises the aliens are vulnerable to the frequency after which they are named, and he plans to use it against them. Requiring a child to act as a transmitter, Jack uses his own grandson, defeating the aliens but killing Steven, who dies from the extreme vibration caused by transmitting the signal.
The prime minister plans to blame events on the US General to save his own career; however, Frobisher's personal assistant, Bridget Spears (Susan Brown) reveals that earlier in the day she retrieved the Torchwood contact lenses and has recorded everything that happened and will release the incriminating footage to the public, ending Green's tenure as prime minister. Six months later, Rhys and Gwen meet with Jack, who has been away travelling the world since the defeat of the 456. Gwen returns his vortex manipulator with a newly-tooled leather wrist strap to him and pleads with him to stay, but Jack states it is time for him to make a new life for himself, and teleports away into space.