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It's four years later, and the children of Earth, including Jennifer, have got it pretty good. Brought up in a world of plenty, they are nearly perfect — physically and mentally. Turns out, some even have telekinetic and psychic powers. But as the younger generation flourishes, the adults aren't faring as well. Ricky for one is dying, painfully, slowly; and the people of New Athens, the keepers of the old way of life, are mobilizing for a possible resistance.
Then the creepy stuff happens. Kids all around the world fall into a kind of trance, raising their right hands towards the sky, hailing and chanting for Jennifer. Some tweens take it one step further, and actually show up at the Greggson's doorstep, looking for their leader. Only she has the power to show them worlds beyond Earth. The Greggson family decides maybe it's time to relocate to New Athens.
New Athens is much like the metropolises we know and love today: they're polluted, smelly, overcrowded, and death is always lingering in an alley somewhere. Not long into their stay, the Greggson family is brought before the mayor of New Athens, Jerry Hallcross, who gives them a special tour, and takes them to their new home.
Jake and Milo, who met at the World Federation party in South Africa, chew the fat over tablet devices. Jake humors Milo's request to ask Jennifer a few questions about her abilities — and to tell him the fate of mankind. She leaves him with the chilling message, "The end begins," as well as a flash of what's to come: the utter destruction of planets. With this new information, Milo vows to sneak onto The Overlords' vessel with the next shipment of animals. His beloved Rachel is heartbroken that he's leaving and reluctantly agrees to help him.
In his time of agony, Ricky is transported back to his honeymoon suite where he gets to live out that happy memory with his dead, first wife Annabelle. But when all the fun has run out, he realizes it is only fantasy. And after thinking long and hard about it, Ricky finally lets Annabelle, and that memory; go, once and for all.
Meanwhile, Karellen addresses the people of Earth one last time, to tell them that they will be evolving into the next generation of being (as in eventually they'll all die). Oh, and Karellen also informs them that the children will all leave them and become superhuman. Ripped from their parents' arms, the young ones begin floating upwards into the sky — all, except for Tom Greggson. The three remaining Greggsons go in search of Jerry Hallcross, hoping they can intercept him before he blows up New Athens. Without children to raise, Jerry and others no longer have a reason to live.
At the church in the cemetery where his daughter is buried, a drunk Jerry is ready to obliterate New Athens and go down with the ship. After a long goodbye, Tom, too, joins the other children as part of The Overlords' greater mission, leaving his parents and all the others of New Athens to perish in the explosion.
Up on The Overlords' ship, Milo is granted a warm welcome by one of The Overlords. He shows Milo their home planet, and takes him to The Overmind — the collective consciousness of the universe. In a white space, the Overmind tells Milo that the children have moved on, and that the rest of the humans will be integrated into the cognitive melting pot. It's a lot for Milo to handle, and he passes out.
When he wakes up, its 80 years later and Earth is abandoned, all of humanity having died out. But The Overlords did Milo a solid, and retrieved Rachel's aged, frozen corpse from the rubble. Milo accidentally shatters it to pieces. Karellen consoles the grieving Milo and assures him that Rachel continues to exist as a figment in Milo's mind. But rather than living out the rest of his days on The Overlords' vessel, Milo volunteers to return to Earth and report back findings of interest.
Before Jennifer sucks up all the energy from what's left of the Earth, Milo begs The Overlords to safeguard a memento. They play for Milo his memories, allowing him to relive his life, sounds, visions, and feelings. And for that brief moment, right before the world explodes, Milo harkened back to a simpler time—a world without Utopia.