Scotland in 1965.
Jack drives up and meets with a woman who confirms they are at the coordinates specified by the aliens designated 456. She explains that in four months the virus will mutate and it could claim up to 25 million people. The 456 will offer the antivirus in exchange for 12 children. Jack admits it's a good deal and the woman confirms that the children will live forever. She tells Jack that they need him to deliver the children because he doesn't care.
Jack tells Gwen and the others that he handed over the twelve children. Clement remembers Jack calling himself their uncle and telling the children they were going on an adventure. He took them toward the light but Young Clem held back until Jack told him it was safe. Young Clem went forward but ran away into the fields when the light flared. The 456 delivered the antivirus as promised.
Clement tells Jack that he's been in every nightmare that he ever had. He grabs a gun and shoots Jack dead, and then accuses all of them of being involved. Gwen takes the gun and calms him down, but Clement warns that the 456 want the children and Jack took them to him. Jack resurrects, scaring Clement into running further into the warehouse. Gwen goes after him and hugs him. Meanwhile, Ianto asks Jack why he didn't mention it before. Jack admits he doesn't recognize the signs at first but Ianto notes that is not what he meant. Gwen brings Clement back and the old man notes that the man who sent his friends to die can't die himself.
Johnson takes Alice and Steven to a cell at Ashton Down. Alice warns that if they anger Jack, he'll hunt them down and kill them all. She admits to Johnson that's the reason she's stayed away from Jack all these years is because he can't die, and has nothing to fear.
Jack admits to Gwen that he figured that the 456 were running a protection racket but they had no choice. He explains that Clement and the others wouldn't have been missed because they were orphans. Clement wonders why he was left behind and Gwen suggests he wasn't quite old enough to meet the 456's criteria of pre-pubescent children. The team continues to watch through Lisa's contact lenses as the diplomatic staff return to Room 413 to meet with the 456 again. Frobisher asks the 456 for clarification on what they intend to do with the children. The 456 say that some "remnant" is watching, and Clement thinks it's referring to him. Gwen tries to reassure him while Frobisher says that the Prime Minister is watching via a camera. Once the 456 is reassured that its response is off the record, it invites Frobisher into the containment chamber with the Prime Minister's camera. Clement tells the team that the creature is hiding something.
A cameraman is equipped with a protective suit and sent into the containment room via an airlock. He gets footage of wormlike aliens and Dekker monitors the biosigns. He informs Frobisher and the others that there are three distinct forms of life inside of the room. The cameraman comes face-to-face with a mutated human child and Clement sobs in terror. The American representative, General Pierce, wonders where the 456 got a human child. At the Hub, Rhys wonders if the child knows what has been done with it. Frobisher demands to know what the 456 have done with the child. The aliens go berserk and start repeating Frobisher's words about smooth diplomatic relations. They get the cameraman out of the containment chamber while Frobisher tells the 456 that the deal is unacceptable. The 456 insist that they don't harm the children and they feel no panic. It assures Frobisher that the children live a long life, but Jack wonders what the aliens want them for. The 456 then say that the world has one day to turn over 10% of their children, or they'll wipe out the entire human species.
In the conference room, Pierce asks Brian Green if Britain has had dealings with the 456 before. Green admits it's happened but that he wasn't involved in 1965. Pierce notes that he kept the previous negotiations secret and Green admits that it was convenient. The American demands all of the 1965 files immediately and warns that the UN will decide what measures to take against him.
Come the morning, Ianto talks to Jack and notes that the guilt must have been eating away at him. Jack says there's nothing Ianto could have done, but Ianto wonders if Jack is keeping other secrets about what he's done in the past. Jack insists that's all there is but Ianto says that he simply pretends that's all there is. As Jack leaves, Ianto accuses him of keeping secrets again. Jack explains that he's going to call Frobisher and needs to go out. As he goes, he tells Ianto that Frobisher took Alice and Steven hostage to ensure his good behavior.
Frobisher tells his staff to take a break and Jack calls him. Jack offers to put things right and work together. Frobisher responds by asking him to give himself up while his people trace the call. Jack warns that the 456 want more children, possibly millions, and he'll tell the world to stop them. He cuts off just before the trace is completed. Bridget suggests he get some sleep but Lois informs Frobisher that the Prime Minister wants to see him. She accompanies Frobisher to the Gold Command meeting room and Torchwood watches on Lois' monitor. As they watch, Gwen promises Jack that they'll get his family out.
Green informs his staff that they're going to try and bargain with the 456 over the number of children. UNIT warns that they can't detect the 456's orbital military base that must surely exist. Green calls upon Frobisher to calculate how many they children they can reasonably give up and camouflage the losses. Frobisher starts going over immigration files of failed asylum seekers and determines they can spare 60 "units." Green tells him to go back and tell the 456 what they are willing to give. Frobisher goes back to Thames House and calls his wife Anna en route. He tells her that there's nothing to worry about and she'll have to trust him. She confirms that the bodyguards arrived and Frobisher tells her that he loves her and the daughters and will be home soon. As he rings off, Anna says that she loves him too.
Frobisher and Dekker return to Room 413 while Lois watches from the conference room. Frobisher tells the 456 that they can only take 6,700 children, one per million population and 62 from the UK alone. The 456 inform him that it is not acceptable but Frobisher leaves to give them some time to think about it. The 456 start reciting the number 3.2.5,0.0.0.
Johnny and Rhiannon continue to take care of the neighbor children. They go into a trance and start reciting 325,000 in chorus, along with Clement and all the children of Britain. The children in the U.S. say 2,3,4,0,0,0,0. The world governments determine that the numbers are 10% of that country's population. Brian realizes that the 456 have rejected their final offer and calls for a break. One of his aides, Rick Yates, notes that that a 10% culling could be spun to the world based on the demands of a growing population.
When Johnson's people can't find a trace of Jack, Johnson takes a squad to London.
Brian Green tells his people that they have no choice and must address the practical questions. They wonder how they would select the children and Green leaves it to Frobisher. He starts proposing transportation solutions and then turns it back over to Green to determine the criteria for selection. They begin to argue, noting there is no criteria that anyone could settle on and they have little time to choose. One of the women, Denise Riley, insists that she won't let her children go and it's generally agreed that Gold Command's children would be exempt. Clement, listening in, notes they're a gang of bastards. Green says that he'll make the final decision but assures them that the children and grandchildren will be exempt. When they argue over the exemption of other relatives, Denise insists that their first responsibility is to protect the best interests of the country. She points out they must discriminate between those who are vital to the nation's interests and those who aren't. She says that they must choose the children from failing schools, those with no likely future, and use the school league tables to choose. When nobody speaks against her idea, Green accepts her recommendation and tells Frobisher to proceed.
At the Hub, the team decides to use the recorded evidence to get into Thames House and force Frobisher to release Jack's family. Ianto and Jack load up and drive to Thames House. Gwen contacts Lois via the contact lenses and says they need her help to stop them.
The peoples of the world have realized the numbers represent 10% of each country's population and are looking to the UN for answers.
Jack and Ianto are caught in a traffic jam and forced to abandon their car. Ianto calls Rhiannon and tells her that the 456 want children. He tells her not to let anyone take her children away, and she needs to get the word out to everyone possible. Johnson's team tracks the call and Johnson moves in on the signal location. Ianto gives Rhiannon his love and hangs up.
Gwen gives Rhys a laptop and assures him he's the most important part of the entire plan.
Johnson arrive at Ianto's last location but he's long gone. However, her people locate the old Torchwood holding facility nearby and she moves toward it.
Frobisher explains to the board that they'll announce an inoculation program to stop the children from speaking in unison. Once it goes wrong and the children disappear, they'll blame the 456. Ianto calls Gwen as they arrive at Thames House to tell her they've arrived. Johnson's people track the call to Gwen's location at the Torchwood warehouse and move in. Meanwhile, Gwen tells Lois that Jack is in position and she should act now. Lois raises her hand and finally gets Green's attention. She tells everyone that she's representing Torchwood and informs them that all of the meetings have been recorded. Torchwood will make the recordings public unless they do what Torchwood says.
Johnson and her people arrive at the warehouse and break in. They find Gwen and Clement.
Jack and Ianto enter Thames House and put their guns down.
Gwen tells Johnson that they've been expecting her and she's to take Gwen to Alice and Steven. When Johnson threatens to shoot her while resisting arrest, Gwen shows her the recordings.
Lois explains that Jack has entered the MI5 reception building and Green is to let him deal with the 456.
Gwen lays it out for Johnson and explains that Rhys is at a secret location with a laptop, and he will send the recordings unless Johnson and the others do what Torchwood says.
Jack and Ianto take the elevator up to Room 413 and have Dekker set up a camera for a live feed. They enter the containment room and Jack tells them they won't get what they want. When the 456 point out he yielded in the past, Jack admits he made the trade in 1965 but will never let it happen again. The 456 insist they will yield again but Jack points out the numbers are too large this time to keep the disappearances a secret. He tells the 456 to leave the planet for good or the humans will rise up against them when they learn the truth, and Jack will lead them. Ianto tells them to check their records on Jack Harkness and realizes who they're facing.
At the Torchwood Hub, Clement realizes that the 456 can sense him.
The 456 notes that humans have adapted to infant mortality rates before, but Jack informs it that they're adapting by declaring war. The aliens announce that the fight is to begin and tells them that action has been taken. The building seals off as alarms go off, trapping Ianto and Jack in the containment room. It tells them that a virus has been released which will kill everyone in the building. Frobisher confirms that nothing can get in or out. Jack tells the guards to seal the air conditioning and hand out oxygen equipment, while the occupants panic.
In the containment room, Ianto draws his guns and tells the 456 to give him the antivirus or he'll blast a hole in the containment wall. Jack returns and tells them to yield, but the aliens point out that they're dying even now. The containment wall is proof against their bullets and the speakers start giving off a screeching noise.
At the Hub, Clement goes into convulsions as he hears the transmitted sound.
Ianto realizes that he's dying and collapses. Jack says he'll take it all back as long as Ianto lives.
Clement screams in agony as blood pours from his nose and ears. The 456 announce that the "remnant" will be disconnected and continues to make the screeching noise. Clement finally dies in Gwen's arms.
Dekker runs to get a hazmat suit and protects himself just in time. The other building occupants pound on the doors but there's no escape and they die one by one.
Jack tells Ianto that it's his fault, but Ianto says it isn't He asks if Jack will remember him in a thousand years' time and Jack assures him that he will. Ianto dies and the 456 tells Jack that he will die and his people will deliver the children the next day. Jack kisses Ianto one last time and then dies himself.
Green, Frobisher, and the others watch on the monitors. They realize they have two choices: they go to war against an enemy they can't beat, or they go to war against their own people for their own good. All they can do is choose between 35 million children or 6.7 billion people. Green tells Frobisher to put the plan into effect.
Later, Johnson's people take Gwen to see the corpses of Jack and Ianto. Jack resurrects and finds Gwen crying over Ianto's body. He hugs her and she admits there's nothing they can do.