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.

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.

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

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.

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 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.

Molly and JD try to convince Shepherd to broker a peace between humans and hybrids. Meanwhile, Lucy tries to manipulate Charlie’s feelings to put him in a compromising position.

Following a near-death experience, Molly has a harrowing vision she can’t shake. Also, Shepherd's loyalty to the Global Space Commission is called into question.

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.