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.

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.

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, 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.

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