Shayna and Toby discuss the fact that 58 pregnant women have died in 4 months.
JD begins to have sex with a woman. Molly interrupts, showing up at his house. JD's lady friend leaves when she sees Molly.
Ethan cleans his scooter and thanks Lucy for getting it back for him. He tells her that Charlie told him Molly was a woman that he must have seen on TV, that he didn't actually know her. Lucy tries to convince Ethan that Charlie and Julie are hiding something from him.
JD goes back to Molly's house and she explains about the "Ethan was here" message. JD scans Molly's security system (which was wiped clean) and ID's Charlie as the one who deleted the security footage.
Lucy goes to a club, moves in on a guy by seducing him, and then assassinates him. It's revealed that this is not real, only a combat simulation. Julie, Anna, and Charlie are glad that she acted well, without hesitation, passing her "basic training" test.
Julie and Anna discuss the problem with Ethan because Anna and her people found out that Ethan disabled his GPS while Julie was away. She warns Julie that she needs to take care of Ethan, perhaps installing limiters in him.
Shayna tells Toby that they need Molly to come back and work on the virus; what she did last week was basically like uncovering a decoder ring in a box of "junk DNA." Shayna tries to coax Toby to quit, saying they could quit and have babies. Toby tells her that's insane. Shayna is offended and makes a comment about his attraction to Molly.
Julie confronts Charlie about what happened with Ethan when she was away. Molly and JD show up at Julie's. She sees Ethan there and embraces him. She realizes that Julie did something to Ethan's memory. She attacks Julie, who calls the police. Molly warns Julie that she'll be back for her, and they leave.
JD and Molly try to figure out how Julie was given custody of Ethan.
Ethan confronts Julie about having erased his memory. She explains that she did it because he was sad. She tries to embrace him but he rejects her, requesting Lucy.
Molly listens to John's last message with JD. They go over the timeline of events between Ethan being taken and him winding up with Julie. JD connects the dots to Molly testifying at Congress. Molly realizes that John's death may not have been an accident. She offers JD money to help her figure it all out.
Molly goes to confront Toby about how Julie wound up with Ethan. He says it's complicated. She insinuates that John's death was part of the government conspiracy. Toby denies it. She threatens him with telling the truth to the press unless he helps her get Ethan back. He refuses, and she leaves. Toby reports to Shayna that they have a problem.
JD goes to visit someone who calls him Sarge and he calls the guy Private. The man is on benefits and puts on some kind of "act" to continue getting them. He agrees to help JD with Molly's case into John's death. JD shows him John's car's "black box" and asks for help in figuring out who tampered with the car and what exactly happened.
Ethan tells Lucy about what happened and the lies. She insists that what Julie did was wrong. Lucy asks him if he wants to play a game -- she mimics Ethan's voice and tells Ethan how to mimic hers. They speak to each other in each other's voices.
Madame Secretary and Anna visit Toby. Anna Schaefer explains that Ethan was not shut down as was intended of all Humanichs 4.0 and higher, because they needed to cut a deal with Julie in order to secure her involvement in the program. Toby tries to convince them to let Ethan be returned to Molly. Anna refuses and says that Julie will walk from the program. Madame Secretary says she will delegate this to Taylor.
Fiona Stanton, Head of HomeSec, calls Julie and says she wants to meet with Ethan tonight. Julie is upset, thinking they'll take Ethan. Charlie apologizes for what has happened and Julie asks him to leave.
Molly looks at and cries over old family photos of John and Ethan. JD calls her to make sure she's okay and tells her that he's on the case about John. He tells her she isn't alone. She says she's losing it and he says he's on his way.
Fiona and Ethan meet. She questions him on himself. He explains that what he thought was true about himself wasn't. He explains that his brain is like a harddrive-- things can be deleted but never completely erased. She asks how he feels and he says he feels sad and angry.
Toby expresses to Shayna his guilt over what they did to Molly, and explains why he feels it's important to get Ethan back to her.
Toby visits Molly and explains what happened with Ethan. He explains that it haunted him. He tells her that he arranged a meeting with Fiona so Molly can plead her case to get Ethan back. Molly starts having warped vision and having a sex-crazed episode. Toby responds in kind. They are interrupted by JD who cracks a joke. Molly tells him to leave, and he does with some warning. She then tells Toby to go as well.
The next morning, Molly sees a stamp on her hand and recalls going to a club the night before. She rushes out to her meeting with Fiona Stanton and Julie.
Fiona questions Julie about her time with Ethan. Molly flies off the handle at Julie's accusations and accuses Julie of having killed John and stolen Ethan because John dumped her.
Lucy and Charlie discuss the possibility of Julie losing Ethan. She convinces him to take her up the street for food.
JD and his friend/soldier continue looking into what happened with John's car. His friend also uncovers the cell phone records. Julie made an outgoing call to someone in a top-level security position, at an encrypted number. JD is now suspicious of Julie.
Toby tries to take Molly to dinner. She tells him that what happened between them (the kiss) was a mistake.
Lucy argues that free will makes her a better soldier. Lucy auto-detects another restaurant guest's body temperature is suspiciously low at 80.6 and snaps into action. She nonchalantly fatally stabs him with a knife, unseen by anyone, and walks away.
Toby goes to his niece's seventh birthday party to drop off her present. His sister notices he is acting oddly and Toby comments that he does his job so kids can have birthday parties.
Fiona acknowledges that, though Ethan isn't a human being in the eyes of a law, she will treat Ethan as a human with human feelings. Fiona delivers the verdict that it will be in Ethan's best interest to be returned to Molly.
Toby calls Shayna into his office and breaks up with her, they are interrupted by another government personnel who says they are both needed right away.
Molly goes to visit with Ethan. She tells him he won't be reprogrammed again, as they'll make new memories. Ethan tells Molly about Lucy, worried about what will happen with her.
Fiona gathers everyone to say that Lucy made her first confirmed hybrid kill. Everyone cheers and is happy, except for Julie and Charlie who look slightly uncomfortable.
Molly is approached on the street by someone she had sex with in a bathroom stall earlier. As JD approaches, the one night stand attacks Molly. She pushes him off and a mark appears on the man as her eyes go yellow -- she causes him to hallucinate his dead mother, run into the street, and get hit by a car.