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It's the year 2035, and Earth has become a paradise. Milo, now a grown man, has been laid off from his astrophysics post after all space programs were terminated. But before he leaves the lab, Milo makes sure to pocket a few hard drives' worth of data on the Overlords, mostly star maps.
Karellen pays Ricky a visit to his farmhouse, and gives him some tough news — that the Earth has a new destiny. Meanwhile at a large research facility in South Africa, Karellen has gifted Dr. Rupert Boyce a new building, inside which is a device that looks like a massive Ouija board. Milo (who's working there now) tells Dr. Boyce he's seen lab and wild animals exhibiting creepy behavior, their eyes glowing green; but the doctor seems only concerned with persuading Karellen to invite him to his exo-planet.
The Overlords visit the Greggson family, comprised of Jake, Amy and little Tommy who we saw at the end of Part 1. Jake and Amy were childhood sweethearts when The Overlords first arrived. Little Tommy starts acting strangely, causing him to act aggressively and strangely. His concerned parents take him to counselor Peretta — the child of a missionary struggling to find the place of her own faith in a time when God is not needed. During their first session, Tommy tells Peretta all about apocalyptic visions he has. When she asks too many questions, the voices in Tommy's head drive him off the deep end, and he (or the voices?) manipulate space to strangle Peretta with the crucifix she wears around her neck. Peretta takes the hint, and high-tails it out of there. She didn't even ask for a copay.
After suffering a massive stroke, Ricky is transported to a hospital where the doctors give him a grim prognosis. Apparently, there was something in Karellen's ship that poisoned Ricky, leaving him with little time on Earth. Tommy's mother Amy, on the other hand, learns that she will be giving birth soon…to a girl named Jennifer. Strangely enough, Tommy knew what name his mother was going to choose for their new child and also announced the pregnancy before Amy realized that she had conceived.
In the run-up to a reception at his game-reserve in South Africa, Dr. Boyce sends for the Greggsons in California to attend on the pretense of interviewing Jake for a job. Yet, following strict orders from Karellen, Dr. Boyce is really after Jake's wife, son, and unborn daughter. Milo, invited to the event by his date Dr. Rachel Osaka, is giddy to meet Karellen, who's the V.I.P. for the night. When they take the stage, Dr. Boyce and Karellen inform the attendees that they've been shipping animals to Karellen's home planet to be installed in a zoo there.
After the fete, Karellen meets with Amy in the chamber with the Ouija board, and has her place her hand on it. This enables Karellen to communicate with the entity growing inside her, and use it to blast a message to the skies. When Dr. Boyce tries to extricate Amy from Karellen's grasp, she hurls him across the room. Meanwhile, Tom is acting strange himself: he throws his father against a wall, and rushes to the roof of the building only to throw himself off it.
Luckily, Tom is able to hover just feet above the ground and avoid a splattering death. Milo figures out what's going on: Karellen was using Amy and the Ouija board to convey a message in his native language back up to interstellar receptors. He discovers that the symbol Karellen was broadcasting in the sky was of the constellation Carina…The Overlords' home world.
Having left South Africa, Karellen travels back to Missouri to pay Ricky and Ellie a very important visit, and give him a vial of medicine. He also drops a truth bomb: it wasn't the illness that sterilized Ricky…it was Karellen. He did this out of kindness: the Earth's days are numbered, and those with children feel the hurt more than those without. Peretta, who's snuck into the barn, isn't buying any of Karellen's excuses — so she blows him to smithereens with a shotgun.
Without thinking, Ricky injects Karellen with the vial of miracle medicine he was to use on himself, thus bringing back the Supervisor from the brink of death. And with his second life, Karellen smacks down the murderous Peretta and her faith. Perhaps out of desperation, Peretta subsequently takes her own life, just as Amy is bringing a new one into the world — Jennifer, who has piercing green eyes that glow like Christmas tree ornaments.