In 1965, a busload of children was taken out into the middle of nowhere. One of them, a young boy, is seen being scared for his life.
Present Day. Some children start standing eerily still and staring vacantly off into the distance, but the incident ends just as fast as it begins. Gwen notices this while withdrawing cash from an ATM machine and goes to the Hub to investigate, discovering it's happened all over the United Kingdom, blowing a kiss to a photo of dearly departed teammates and friends Owen and Tosh in her office workspace. Jack and Ianto investigate a death by alien parasite, and pass themselves off as the victim's nice gay neighbours in order to get close to the corpse. They get caught by Dr. Rupesh Patanjali, and when he realises that they're alien-hunters, he asks them to help them figure out why corpses have gone missing. Since they need a new doctor in Torchwood, Gwen, Ianto and Jack subtly lead him to the Hub to see if he'd be a good addition for the team.
However, before they get anywhere, all children on the entire planet start chanting in unison. "We. We are. We are coming." They all chant in English, too, and Rhys notices that their chanting is timed with British school commutes and lunch breaks. Jack calls UNIT for help, but Martha Jones is on vacation and no one's cooperating very much.
One elderly man, Clement McDonald, is also chanting along. Gwen goes to visit him in the asylum he's in, and since he was Touched by Vorlons as a young boy, he's able to tell her that she's pregnant.
Home Office Permanent Secretary John Frobisher is worried about his children. He's even more worried when he realizes that he knows exactly what aliens might be behind this: unseen monsters that appeared on radio frequency 456 many years before. And that his job, in the words of Prime Minister Green, makes him a nice public face... and expendable. His plucky new office girl, Lois Habiba, is having a very confusing first day, and his weary personal assistant, Mrs. Bridget Spears, tries to make sense of it all.
Ianto is a bit bothered by appearing as Jack's boyfriend in public. Jack doesn't see the issue — they are a couple. Worried about the children, Ianto visits his sister to check on his niece and nephew, and is unexpectedly coaxed out of the closet by her. He explains that it's "not all men, just Jack". That he's not sure what it is yet. That's he's not broadcasting it to the world. Jack visits family too: his daughter Alice, who is very happy being a regular middle-aged single mom and not having any aliens in her life. She'd rather not have her dad in her life too much either, as it would only confuse her son.
Dr. Rupesh Patanjali turns out to have been a mole, and he's ordered by the government's local anti-terrorist squad (led by Agent Johnson, who, as Andy remarks, is pretty hot) to kill Jack. Rupesh does, and Agent Johnson plants a bomb in Jack's stomach. He wakes up shortly afterwards, naturally escapes and heads back to the Hub.
Gwen takes a quick pregnancy test at the Hub, and Jack puts his hand on hers when he congratulates her. The automatic scanner immediately shows the bomb inside him. Gwen races out, Ianto passionately kisses Jack goodbye, and Jack stays behind to let the bomb explode inside him — destroying the Hub completely. Fridge Horror abounds - all that cool alien tech they had is toast, Janet and all the Weevils in lock-up have probably been turned to puppy chow, along with the bodies in the morgue (maybe not Gray - we never saw exactly where he ended up; otherwise, Jack just lost his brother for good), and if Myfawny ever pays a visit to her old stomping grounds, all she'll find now is a burnt out hole in the ground. And while all of this is happening, all the children have once again begun to repeat the words, but their final repetition adds a new one.
"We are coming... back."