Astronaut Molly Woods tries to reconnect with her husband, John, and son, Ethan, after returning from a 13-month solo mission in outer space. Molly's mystifying experiences in space lead to events that will ultimately change the course of human history.

After Molly collapses and experiences a vision of her encounter on the Seraphim, Sam agrees to give her an ultrasound so she can learn more about her mysterious pregnancy. Also, Molly tracks down Kryger and he reveals the disturbing details of his own solo mission that the International Space Exploration Agency (ISEA) is keeping secret.

Molly has to decide if she is going to reveal her pregnancy to John after he confronts her about her distant behavior. Meanwhile, John and Molly face parents who are suspicious of Ethan when he goes to school for the first time.

After Sparks attempts to quarantine Molly, she and her family seek refuge on a remote island with her estranged father, Quinn. When the agency closes in on their whereabouts, Ethan is exposed to grave danger. Meanwhile, Yasumoto experiments with a strange and deadly substance.

John begins to doubt Molly's mental state when the validity of her pregnancy is questioned. Meanwhile, Ethan suffers a serious setback, and John and Julie disagree over how to care for him.

Molly uncovers footage that may reveal the real reason the ISEA chose her for the solo mission, on EXTANT. Meanwhile Ethan experiences his first dream, an unforeseen advancement for which he was not programmed, and Julie distracts herself from work with a mysterious man she meets at the gym.

Convinced the agency has her baby, Molly is determined to find out where. Meanwhile, John discovers new and startling advancements in Ethan's programming, and Kern holds Kryger hostage in an attempt to recover the incriminating video he stole from the ISEA.

When Molly learns that her baby is alive, she sets out with Kern and Kryger to devise a plan to intercept the baby before Sparks and Yasumoto can relocate him. Meanwhile, John struggles to keep up with Ethan's rapid development.

When Sparks falls under the influence of the vision of his deceased daughter, he flees with Molly's baby to a remote location. Now, Yasumoto and Molly must rely on each other to track down the offspring.

As Molly gets closer to finding her "offspring", John learns that Yasumoto might not have his family's best interests at heart, and Sparks commits to do whatever it takes to keep the "offspring" alive and maintain the visions of his dead daughter.

As the offspring's powers grow, Molly learns of Yasumoto's painful path to immortality. When Sparks starts to have doubts about the mission, Anya takes charge. Meanwhile, Odin tries to secretly access Ethan's circuitry.

When Molly finally comes face-to-face with her offspring, she realizes she may be the only one who can stop the coming danger. Meanwhile, Julie uncovers grave secrets about Odin.

Molly returns to space in an attempt redirect the Seraphim away from Earth and protect the world's population from the deadly spores. Also, John discovers that Odin's plan has put Ethan in terrible danger.