Molly watches a news broadcast about a virus spread in vitro -- the EVH-789 virus. She flashes back to earlier, when she shot Toby. Toby survived because he wore his bullet proof vest.
Charlie baby-sits Lucy and Ethan while Julie is in DC on business. Lucy is upset that she couldn't go with Julie. Ethan has a memory flash of Molly's face in a picture of Ethan and Julie. He purposely doesn't tell Charlie when Charlie asks him what's wrong.
Toby has gathered genetic code-breakers to find "a biological needle in a haystack" -- a virus to eradicate the alien-human hybrids but leave humans unaffected. Toby and Molly discuss what they are doing with the pregnant women. The women are being quarantined and tested on.
The warning about EVH-789 virus plays through a hospital where JD is. A nurse tells him to get out because it is a restricted area. He grabs a pamphlet on his way out and leaves with his daughter because he realizes it's a quarantine site.
Toby and Shayna argue about his bringing Molly onto the virus team. She believes Molly shot Toby on purpose, to protect her son. Toby thinks Shayna is blinded by her dislike of Molly, while she thinks he's blinded by his love for her.
Ethan is looking at pictures of Molly in his room. Lucy sees and asks who it is. Ethan only knows that her name is Molly. Lucy suggests that he go find Molly.
Back at the virus team lab, Molly works on the virus. She has a "possessed" moment again. Nate, a fellow virus team member, realizes she's found something in the discarded DNA.
Ethan sneaks out of bed and takes a phone. He calls Molly, who ignores the call because she's flirting with an unwitting man at a fast food place.
The next morning, Molly is woken up by JD knocking at her door. She rolls over and notices a man in bed with her and yelps. She kicks him out and talks to JD, who asks for a favor. He tells her that his daughter is pregnant.
Charlie and Lucy realize Ethan is gone. When Charlie tries to track him via his built-in GPS, Ethan turns it off.
Back at JD's home, Molly draws blood from Kelsey and asks about Kelsey's symptoms. Kelsey gets nervous that her headaches are a bad sign for her prognosis.
As Molly leaves, she spaces out again and JD notices. She comes clean to him about her symptoms and blackouts. She refuses to go to a doctor because of her experience at ResWell. JD suggests he be her keeper, but she refuses, saying he's already looking after his daughter.
Ethan goes to his old burned down house. He gets Molly's new address off of a construction worker who finds him there.
Nate says that the spores are chimeric, having capacity for male and female organs. They discuss the danger to the pregnant subjects.
Kelsey tries to leave to go to the clinic and reveals she found out who Molly really is. They argue about how JD left their family when she was younger. JD refuses to let her go to the clinic. He shoots out the tires from the car she's in. She gets on a motorcycle instead.
Ethan looks for Molly's new apartment. Some thugs give him directions and then steal his scooter.
At the lab, Molly suggests to Nate that the hybrid DNA might be closer to human DNA then they were thinking. Nate moves the DNA markers around and it creates sound waves. Molly hears something saying "Help me" when she turns on the speakers, but Nate hears nothing.
Molly tells Shayna and Toby about what she found.
Charlie and Lucy continue to track Ethan -- they go to Molly's old house. Ethan, meanwhile, breaks into Molly's current apartment.
Molly is kicked out of the lab. She breaks some things and steals a sample on her way out.
Charlie and Lucy encounter the thugs, realizing they stole the scooter. The thugs threaten Charlie and Lucy takes them out easily.
Ethan finds old pictures of him and Molly in the apartment and shorts out, collapsing.
Molly goes to JD, who tells her that Kelsey took off for the clinic. Molly tells JD that she tested Kelsey's DNA and the baby is normal. JD hugs her. Molly is hit with an "episode" and kisses JD, beginning to undress. JD stops it from proceeding and snaps her out of it.
Kelsey returns and tells JD that he was right; there's something off about the clinic. Molly and JD tell Kelsey the good news, that there isn't anything wrong with her baby. She hugs JD and cries. Molly leaves them to have their moment.
Charlie and Lucy finally track down Ethan, who is still unconscious, his circuits knocked out. Charlie carries him out. Back at home, Lucy tries to convince Charlie not to change her with limiters and bargains that it (and the episode with Ethan) will be their secret from Julie. When Charlie chats with Julie, he lies and says he reinstalled Lucy's software. He tells her he misses her but she doesn't respond in kind.
Julie tells someone unseen that they were right and "it" worked, while reading Machiavelli's "The Prince."
Kelsey sleeps, while JD watches over her, drinking. Julie returns home and secures her house. She notices her nails are weird again while in the shower. Once she gets out of the shower, she sees a note on the mirror saying "Ethan was here."