Gwen records herself relating the events that happened leading to the end of the world.
Prime Minister Green goes on national television and informs parents everywhere that they'll be opening schools so that parents can send their children there. The government will then send representatives to discuss the new inoculation program and answer any questions. Rhiannon and Johnny, aware of the truth thanks to Ianto's warning, tell their children that they won't be going. Rhiannon tells her son to go to the neighbors and pass on the message that the government is using the schools for their own purposes.
Anna Frobisher tells her two daughters that they won't be going to school.
At the government officers, General Pierce tells Bridget Spears that the UN has put him in charge now that the British government has demonstrated that they can't handle the situation. He orders Bridget to brief him and she explains that soldiers will be sent to 2,600 primary schools to transport the children. When Green wonders if the soldiers might mutiny, Pierce tells him that they plan to hold the soldiers' families liable if any of them disobey orders.
Once the building is decontaminated after the release of the 456 virus, Colonel Oduya goes to the 13th floor and finds Dekker waiting for him. The colonel tells the 456 that they're initiating the plan to deliver the children to them. He asks the aliens how they plan to pick up the assembled children and the 456 show him a monitor with the giant beam of light they used to transport down. Oduya wonders why they need children and the 456 explain that they derive a chemical from their bloodstream that they use as a recreational drug. Green is watching on a monitor in his office and turns away in disgust, and Pierce points out that the British Government were the ones who made the initial trade and gave the 456 what they wanted. The general then reluctantly orders the soldiers to go to the schools.
Most of the nation's children go back to school. On the television and radios, the government asks the people to trust them.
Frobisher and Bridge go to the school where the corpses from the MI5 building are stored. Jack revives and Gwen greets him, and Gwen reminds the officials that her threat to release the recorded conversation still stands. Frobisher tells her to go ahead, figuring that there's little she can do to make things. Jack reluctantly agrees with him and gestures to the bodies surrounding them. He tells Gwen to call Rhys and call off the release of the video.
As Gwen talks to Rhys, telling him about how the 456 killed Clem and Ianto, Frobisher informs Jack that Lois is under arrest for espionage. However, he assures Jack that Steven and Alice have been released. Jack confirms that the government hasn't released the news of Ianto's death to Rhiannon and then asks Gwen to deliver the news. He also admits that he can't bear to look at Gwen. Frobisher agrees and arranges for a helicopter to deliver Gwen and Rhys to Rhiannon's home.
Once Gwen and Rhys leave, Frobisher's soldiers put Jack under arrest. They take him to a cell and lock him up next to Lois. She wonders what they're going to do but Jack ignores her.
At Ashtown Down, Johnson releases Alice and Steve and takes them to a monitor. She shows them an image of one of the abducted children from 1965, "stored" within the 456's containment chamber and being used to distill the drug. Johnson warns them that the government will be turning over millions of children to a similar fate in two hours.
Green calls Frobisher to his office and informs him that his children will be chosen for "inoculation" after all. The government wants a high-ranking official's children on hand to prove that they're doing nothing suspicious. Frobisher threatens to go public but Green, unimpressed, merely apologizes and dismisses him. Once he leaves, Frobisher goes to see Bridget and asks for a Requisition 34. She wonders why but he ignores her and takes the case containing the requisition. He then kisses Bridget on the cheek and leaves.
When Gwen and Rhys return to Cardiff, PC Andy welcome them back and drives them to Rhiannon's house. As they drive, Gwen refuses to tell him what's going on. Rhys finally tells Andy that Gwen is pregnant, and Gwen admits that all of the chemicals and radiation she was exposed to with Torchwood negated her birth control measures. When she complains that her life is ruined, Rhys takes offense and she wonders if he wants to have a child in a world like theirs. He insists that she's not getting rid of it but Gwen remains non-committal.
With an hour left until the children are taken away, the troops move into position. Bridget goes to see Lois in her cell and explains that she met Frobisher 30 years ago. She kept an eye on him throughout his career and he finally came to work for her, asking for her by name. Bridget admits that Frobisher wasn't perfect but insists that he worked hard and intended the best. She tells Lois that she wants her to know that Frobisher was a good man and that what happens next isn't her fault, and then leaves.
At home, Frobisher sends his two daughters upstairs and kisses his wife. Once he's alone, he takes a gun, "Requisition 34," out of the case. Frobisher then kills his daughters, and then his wife. Finally, he kills himself.
Rhys waits in the car while Gwen and Andy go in to talk to Rhiannon. She answers the door and explains that she's looking after all of the neighbor children. As they go in, Gwen remembers Jack asking her to save Ianto's niece and nephew.
When the time arrives, Pierce gives the orders to his men in the field. They take away the children, ignoring the objections of teachers and parents.
Gwen tells Rhiannon and Johnny that Ianto is dead. They don't want to hear her explanation but when Rhiannon mentions Ianto's father, Gwen doesn't know about him and Rhiannon angrily tells Gwen that she didn't know Ianto at all.
As Steven plays with some soldiers, Alice watches over him. Johnson comes over and warns her that the operation has begun.
Pierce gets word that children in one of the target areas are staying home and orders his men to move in. Rhys sees them coming and goes inside to warn the others. Gwen vows to get the children away and tells Rhiannon and Johnny that Ianto died trying to stop the government from taking the children away.
Johnson tells Alice that Steven is one of the "nice kids" and won't be taken away. The government is only turning over children from the lower s. The agent insists that she protects the state and was brought up to protect the state, but Alice isn't comforted. She wonders what the world will be like when the other 90% learn what happened, and says that the one person she needs is Jack Harkness.
Soldiers break into the holding facility and take Jack out, ignoring Lois. She can only watch as the soldiers take Jack to the rooftop and leave in a helicopter.
Dekker returns to his office and finds soldiers going through his records. He protests and they knock him out.
While Andy tries to contact police headquarters, Gwen, Rhys, Rhiannon, and Johnny get the children ready to go. When the soldiers break into the front of the house, Johnny hugs Rhiannon briefly and then goes to stall them. The neighbors come out to fight the soldiers and Andy removes his uniform and joins the fray. While the soldiers knock them down, Gwen and Rhys take the children away to a nearby abandoned warehouse.
The soldiers bring Jack to the facility with Dekker, Steven and Alice. They take Steven away and Johnson tell Jack that he needs to find the proper frequency to destroy the 456. When Dekker tells them that it's a waste of time, Johnson casually shoots him in the leg and then asks Jack if his daughter was right about his skills. Jack goes to work with the computer, accessing the Torchwood software, and ignores Dekker when he says that he hacked Torchwood years ago and found nothing useful. Meanwhile, Alice picks up a broadcast from a pirate station that is showing footage of soldiers taking the children to rendezvous spots.
At the warehouse, Gwen records his video log and Rhys asks if she intends to abort their child. Gwen assures him that she would never do that and apologizes for her earlier comments.
Pierce receives the news about the pirate station and the resistance and tells his soldiers to fight back. When they learn that they only have 80% of the millions that they need, Oduya asks the 456 if that is sufficient. The aliens demand the full 100% or promise retaliation, and Pierce authorizes maximum force. As Bridget continues her work, Denise says that she shouldn't be there. Bridget insists that Frobisher would have wanted her on duty and watches Green carefully.
Jack tries to generate a constructive wave that will cause feedback to the 456. Dekker warns that it will have no effect but Jack realizes that the 456 used a frequency to kill Clem by remote. Johnson plays back a recording of the 466's screech at the time of Clem's death and Jack realizes that somehow the feedback hurt them even as they killed Clem. Listening, Dekker admits that the frequency they used is something new.
While soldiers across the country take stricter measures against the resistance, Jack duplicates the necessary frequency. Dekker tells Jack that there's only one way to broadcast the signal: use a human child, just as the 456 does. Alice realizes what Dekker intends and tells Jack to refuse. Johnson warns them that they're almost out of time and Jack has no choice but to go ahead. When she realizes what will happen, a screaming Alice goes to find Steven.
The soldiers approach the warehouse and Rhys and Gwen get the children out of the back. One girl falls behind and tries to hide, but the soldiers find her and take her away.
Johnson's men take Steven out and hold Alice back when she tries to go to her son.
The soldiers close in on Gwen and the others.
Johnson's men place Steven in the resonance projector. When his grandson asks what is going on, Jack ignores him.
Gwen escapes with one child but the soldiers capture the rest along with Rhys and Rhiannon.
A horrified Jack stares at his grandson for a moment and then activates the resonance projector. The boy screeches in pain as he "transmits" and Alice stares at her son in horror. Across the world, the children pick up the signal, amplify it, and feed it back to the 456 that used them as transmitters earlier to deliver their messages.
In Room 413, Oduya looks at the containment chamber. The 456 thrash against the glass in agony and finally explode, while their ship above withdraws the light column.
Crying, Jack watches Steven shake apart from the force of the resonance wave.
Once the 456 representatives are confirmed dead, Oduya reports to Pierce that the alien threat is over.
Once Johnson lets her into the room, Alice runs to her dead son and cradles him in her arms. Sobbing she looks around and begs anyone to help.
Perce salutes the Prime Minister and leaves to clean things up. When Denise asks her superior if he's going to issue a statement, Green says that it should all work out for him since Pierce assumed control, so they can blame him for anything that happened. Disgusted, Bridget points out that Green tried to save his own skin first. She then informs Green that she talked to Lois and learned how to use the Torchwood lenses, and then signed them out under emergency protocols. Bridget has recorded everything Green said and did and is going to release it to the public. When he threatens to have her arrested, Denise steps forward and thanks Bridget for her help. She promises to free Lois and dismisses Bridget, and then tells Green that she'll be taking charge now that he's out.
Alice finds Jack out in the hallway and glares at him for a moment, and then goes back to her son. Jack pauses in remembrance of his grandson for a moment and then walks away.
Six months later, Gwen and Rhys go into the countryside to meet Jack atop a hill. Gwen asks if he's okay and he says that he is, and tells her that he's been traveling for the last six months. Now it reminds him of a graveyard. Gwen asks him to rejoin them but Jack says that he hasn't raveled enough yet and that he's wants to summon a cold-fusion cruiser to pick him up. He explains that he needs his wrist-unit to send a signal to it and Gwen gives it to him. As Jack sends the signal, he says that there's nothing to come back for and Gwen says that he can come back for her. She assures him that what happened isn't his fault but Jack says that it's time for him to find a new life because all of the deaths were because of what he did. As the cruiser arrives overhead, Gwen says that he can't run away, but Jack says that he can and teleports away. As Gwen looks after him and cries, Rhys tells her that it's time to go home.