JD ambushes Tobias in his car by hiding in the backseat, telling him that they need to have a chat.
Shayna interviews a Chinese woman about her hybrid child -- how he rapidly grew and then vanished one day when "they" were calling him.
JD brings Toby to meet with Molly for negotiations.
Ethan speaks with Charlie about how the new Humanichs will be his family. He calls Charlie his BHF (Best Human Friend) and mentions that Charlie never lied to or left him. Charlie begins booting up the Humanichs, mentioning that Julie is in DC at the time. Lucy names one new Humanich Lucas.
Molly tries to reason with Toby, trying to explain that the hybrids are no longer dangerous and imploring Toby to expand his mind. She attempts to convince him to see the hybrids and determine the danger for himself before ordering the genocide. He refuses to budge, so Molly threatens to tell the truth about having lied to Congress about the invasion at Toby's request, which would discredit Toby and ruin him.
Toby, released by Molly and JD, goes straight to assemble a team but is intercepted by Shayna. She shows him the Mei Fong interview, where Mei explains that not only is her son a hybrid, but she is experiencing strange symptoms: the same symptoms as Molly. Mei expresses fear that her son is a demon.
Molly and JD go to JD's weapons shack.
Toby reports back to his team that Molly has requested a detente, to sit down with the hybrids and find a way to coexist in peace. Toby clarifies that there will be no peace, and that he will not sit back and do nothing, presiding over the mass extinction of the human race. Toby clarifies that Molly, having chosen her side, is now to be treated like the enemy.
Molly voices her concern to JD that they are being tracked. JD and Molly turn on the news to see that they have been named as terrorists carrying biological weaponry; Toby destroyed their credibility and initiated a mandatory lockdown for the populace.
At the Humanichs lab, Lucy and Lucas discuss their shared memories. Charlie explains to Ethan that Lucy and the other Humanichs share the same neural programming. Ethan is a bit upset that he doesn't have the same memories. Lucy notices that Charlie has a checklist for Humanichs that includes an expiration date. The Humanichs lab goes on lockdown along with the rest of the populace.
Molly and JD return to the hybrid commune. Ahdu reiterates that they want to live freely, at peace with the humans. Another older male hybrid, voices his opinion that their group should fight back, make their way in the world, allowing humans the option to peacefully coexist or die fighting the integration.
Lucy requests that she be allowed to stay over at Julie's while Julie is out of town, and Charlie agrees. She questions him about the expiration date that she saw. Charlie explains that John Woods, wanting Humanichs to have as organic a human experience as possible, build in a termination point, allowing Humanichs to die as humans do. Lucy reacts with shock and outrage that she will one day die. She tells Charlie that she is reacting this way because she is more human than he realizes.
Nate explains to Shayna and Toby that Mei Fong's odd symptoms are a result of hybrid fetus cells being transferred to the mother during pregnancy, and that Mei will soon be a hybrid (echoing the conclusion Molly had come to earlier). Toby has Nate run the test on their employee database which singles out one other person as having that same abnormality: Molly.
Toby instructs Nate to try out a marrow and plasma transplant on Mei Fong to cure her of her hybrid transformation. Nate questions whether they need her consent, but Shayna clarifies that in her current condition Mei is an enemy of the state and they don't require her permission.
Toby goes to a top-security elevator, going through an arduous process of many tests to enter a top secret room. Toby asks "Taylor" (a homeland security analytic program) to analyze all possible hybrid locations for him.
JD and a hybrid go off to guard the perimeter. The hybrid pokes around in JD's mind, causing him to revisit his war experience. Molly stops the hybrid, but he defends himself by saying that he was just trying to get to know who JD really is, since he is someone who will supposedly be protecting them. JD accuses Molly of stopping her attempts to reverse what is happening to her, and voices his concern that the hybrids are not like them: they are unknowns. He tells Molly that she needs to choose which world she wants to live in and that she can't have both.
Charlie goes to read Ethan a children's book, but Ethan requests a "grown up book" instead. Lucy suggests Huckleberry Finn, which she knows that Julie has been reading. When Charlie goes to get it, he finds Julie's Pyxis Cube of photos of her and John. Charlie reacts in shock at the photos, clearly not having known that John and Julie were together.
Ahdu confronts Molly about her discomfort at the commune. He tells Molly that she can control the side effects, and she may have already noticed that they have begun to subside. He tells Molly that her best chance of survival is to embrace what she is becoming.
Lucy talks with Charlie, who is drinking to numb the pain of seeing the pictures of John and Julie, about why he is upset. She makes a move on Charlie, who resists, saying that it would be illegal. Spyder watches the encounter. Charlie finally stops her, saying it can't happen for so many reasons.
Toby and Shayna watch the news, about how the population is getting annoyed at the lockdown. Toby explains to Shayna that Taylor has yet to find the hybrid location. He mentions that everyone, including JD, has a weakness.
JD watches the news and sees that his daughter Kelsey was taken into custody.
Molly tells Terra a myth about Zeus. Terra mentions that her father said that Molly is their leader. JD interrupts, telling Molly he needs to go help his daughter. Ares, a combative hybrid, tries to prevent JD from leaving. Molly fights back against Ares on JD's behalf, but two other hybrids wreck JD's car, preventing him from leaving.
Toby goes back to Taylor, still trying to determine where the hybrid commune is. Toby asks for Taylor's recommendation on a course of action. Taylor recommends releasing the Humanichs and the virus at once, to the location that Taylor has pinpointed. Toby asks what will happen if they don't release the virus. Taylor predicts that humans will die out at the rate they are currently going.
The next morning, Lucy and the rest of the Humanichs get called up to go to battle against the hybrids. Ethan asks if he can go with her but she shuts him down, saying she doesn't even want to go into battle but that's what she's made for. She tells Ethan that he is not like her and the rest of the Humanichs army.
Toby and Shayna instruct Lucy on the course of action: she and a subordinate will infiltrate and scope out the hybrid's defense and location. Shayna tells Toby that she's put in for a transfer to DC because she will never get what she wants if she stays; she kisses Toby and leaves.
Lucy and Lucas approach the hybrid camp, effortlessly getting past the chain link fence.
Ahdu watches JD as he repairs his car, and notes that he is sorry to see him goes and appreciates what JD has done for the group. Ahdu tells him that he is a good man. JD gives Ahdu advice on remaining under the radar, and they shake hands, preparing to part cordially. As JD is preparing to leave in his repaired car, Molly approaches him. JD explains to her that he can't desert his daughter, but that he hates deserting Molly. She tells him that maybe in a different life things could have been different. She thanks him for everything, and he hugs her and kisses her on the head as she cries.
Lucas and Lucy continue to scope out the premises. They are encountered by Heleos, who attempts to work his alien powers on them and notices they are not human. Lucy quickly knocks him out and they put him in the back of their truck. She reports back to Toby that they found the hybrids.