After a 13-month solo mission in space astronaut Molly Woods tries to reconnect with her husband and their son, who is an artificial intelligence. But the impossible news that she is pregnant prompts Molly to recall a strange encounter on board the Seraphim station.
Molly finds Kryger, who relates a similar and disturbing account of his own solo mission on the Seraphim. Meanwhile John's research project moves forward with new funding, and Ethan explores the notion of extinction.
The Woods take Ethan to orientation at his new school, where they face the concerned parents of other children. Molly's supervisor gives her a cover story about her pregnancy, and John throws a party in honor of Molly's last birthday.
On the run from Sparks and his attempts to quarantine Molly, the family turns to her estranged father. Meanwhile Sam finds herself in danger, and Yasumoto presses for greater risks in experiments with a substance that has potential healing properties.
John questions his wife's mental state after all signs of her pregnancy disappear, and she insists that the ISEA is covering it up. Meanwhile, Julie clashes with John while attempting to repair Ethan.
While Molly finds a way to learn why Sam is lying to her, John is excited when Ethan experiences a dream for which he is not programmed. Kryger orchestrates a break-in at the ISEA, where a research scientist appears to have been taken over by an alien intelligence.
After learning the truth about an earlier ISEA mission Molly is convinced that the agency still has her baby. Kern holds Kryger hostage, and John is mystified when Ethan exhibits inexplicable new behavior.
Molly and her new allies set out to find her baby, while Yasumoto and Sparks plan to move the offspring to a new, more secure location. John discovers that he has lost access to Ethan's neural net, and cannot keep up with his rapid development.
Under the influence of his visions, Sparks helps the offspring escape the ISEA facility. John turns to Yasumoto for help in locating Molly, and Odin gets to know Ethan face-to-face.
Molly sets out with one of Yasumoto's scientists to look for her child -- though John believes that Yasumoto no longer has his family's best interests at heart. Sparks introduces his wife to his vision, and learns that the offspring has an agenda of its own.
After Yasumoto's attempts to neutralize Sparks ends in a deadly shoot-out, Molly tracks him to a motel room in the hopes of catching up with her son. John learns the secret of Yasumoto's condition, and Odin takes advantage of his time alone with Ethan.
Molly discovers that the Seraphim station is off-course and missing because of her actions. Julie grows suspicious of Odin, and on the station Sean is stunned to receive a visitor.
Molly arrives on the Seraphim station with a mission to stop the station's fall to Earth, but soon finds that the alien intelligence is fighting back. Meanwhile John decides to shut down Ethan in order to determine the nature of Odin's tampering.
