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.

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.

Molly reveals disturbing new details about Shepherd’s death to the GSC, and Lucy makes a powerful move against the humans and hybrids that could have devastating global repercussions.

Molly uncovers top-secret footage that reveals the real reason the ISEA chose her for the solo space mission. Meanwhile, Ethan experiences his first dream, an unforeseen event for which he was not programmed; and Julie connects with a mysterious man she meets at a gym.

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 and JD frantically race to the hybrids to stop a Humanich plot that will destroy the human race. Also, Lucy has a shocking realization about the GSC that forces her to question her allegiance and put Ethan at risk.

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 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.

John makes a discovery about Yasumoto as Molly gets closer to locating her offspring; Sparks' visions of his daughter persist.

Six months after her life unraveled and dark secrets were revealed, Molly is confined to a psychiatric hospital when she learns of bizarre deaths that sound eerily similar to those she witnessed in space. When she escapes to investigate, she crosses paths with JD Richter, a determined cop who just signed on to the case.

As Molly succumbs to the virus, long forgotten memories surface. Also, Julie is confronted with hard choices and the Hybrids seek revenge.

Molly and J.D. discover another pregnant woman who is suffering from inexplicable and fatal symptoms. Meanwhile, Molly begins to question her own mental stability. Julie struggles with Ethan's rebellion.

Molly finally learns the frightening truth about what happened to her son. Also, Julie’s decision to erase Ethan’s memory has disturbing consequences.

As Molly works to create a virus that will eradicate alien hybrids, she discovers that aliens are trying to communicate with humans through a hidden message in their DNA. Also, Lucy helps Ethan run away from Charlie in order to help him recover memories of his mother, Molly.

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 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.