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. Jeffrey Dean Morgan joins the cast as JD Richter.

Molly and JD discover another pregnant woman suffering from inexplicable and fatal symptoms, while Molly begins to question her own mental stability. Meanwhile, 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.

Molly discovers Ethan is alive and sets out to get her son back. Also, suspicions about John's death cause JD to investigate Julie's potential involvement.

Molly panics when she discovers she is changing physically, the question is into what, and whether she can reverse what's happening to her. Also, JD's ex-wife, Dorothy (Melina Kanakaredes), shows up suddenly on his doorstep to discuss their daughter. 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.

After a Global Security Commission raid on the hybrid compound, Molly desperately tries to save her son Adhu, while JD attempts to rescue his daughter who is being held captive by Shepherd. Meanwhile, Lucy becomes more of a threat to humans.

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

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, JD and Ethan track down John's mysterious former colleague who may hold the key to stopping the Humanich threat. Also, Julie enlists Charlie on a mission to find out where Lucy's orders are coming.

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 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.