The premiere opens on Molly at a mental health in-patient facility, about six months after the events of the season one finale. Molly is enjoying her daily session of virtual reality: first, she imagines have sex in the shower, then abruptly requests that the virtual reality apparatus abruptly switch to a memory of Molly and Ethan playing in his room and talking about getting ice cream. In the middle of the session, Molly is interrupted by a robotic voice informing her that her session is over and it's time for her meds. She tears up at being pulled from the good memory.
We suddenly switch to a time six months earlier. A couple with a young infant find Molly's Offspring wandering the side of the rode, presumably shortly after the events of the finale episode. They bring him back to their home, where they phone the police and report the apparently runaway child that they've found. Alone with the couple's crying baby, the Offspring first soothes the child with a colorful baby mobile vision and then begins twitching uncontrollably and unnaturally as the baby begins to cry even louder. Menacing.
The baby's parents hear its cries and run to find it. The baby appears to be okay, but Molly's Offspring lies on their floor, presumably dead.
Four weeks later, Molly is appearing in front of the Senate Investigation Hearing on Extraterrestrial Life Forms. Molly and the Senate revisit the events of the finale, and Molly lies that she was not affected by the alien spores and that the alien life forms were destroyed. Molly confirms for the Senate that there is life out there, but tells them that no alien life forms have set foot on earth. The Senate congratulates and thanks her, applauding her heroism.
Toby and Molly discuss the fact that she lied under oath. She asks him whether her Offspring is definitely dead. He assures her that he is definitely dead, and that he had some kind of seizure right after the couple picked him up. Toby confirms that they have the Offspring's body and offers to show it to her if she feels she needs to see it. Toby mentions the time he proposed to Molly at her and John's wedding, making very clear there is residual sexual tension between them. He asks where John is and Molly comments that he is where he always is: his lab.
Back at the Humanichs lab, John and Julie are working to rebuild Ethan (and flirting with one another). John explains that Ethan's consciousness was largely in tact, so it was easy enough to rebuild him in a new body. They boot Ethan 2.0 up, enjoy a happy and emotional reunion, and take him home. Julie, feeling uncomfortable and ignored, walks away, perturbed.
Back at home, John and Molly put Ethan to bed. They ask Ethan where he was while he didn't have a body. He compares his experience to being like a bird, not tethered to anything. John confirms that apparently Ethan cannot die. Ethan is concerned that it's because he isn't a human. Molly insists that Ethan has more humanity than most humans, and that that's what's important.
Later that night, Molly lies sleepless next to John, something clearly bothering her. She gets up and, over a glass of wine, reviews the security footage from the week before she returned from space. She seeks and finds confirmation of John and Julie's affair. She becomes visibly upset, but doesn't seem surprised.
John finds Molly viewing the footage and insists that the affair is long over. John argues that Molly had not been invested in their marriage for a long time and maybe never really was. Molly counters that that isn't a valid excuse and that he should have said something rather than engage in an affair. In the middle of their heated argument, government agents bust in with a court order and declare that they have orders to seize the Humanich -- Ethan. Though Molly and John put up a fight, they take Ethan away. John and Molly head directly to Toby, who confirms that the court order is solid. The government sees Ethan as a threat to national security, and their seizure of him cannot be fought against. Molly wonders aloud how they could repay her lying under oath for her country by taking her son.
Meanwhile, Ethan manipulates his guard's taser in an attempt to escape. He encounters Julie, who says "Hello, Rabbit," and stops him from escaping.
Back at their home, Molly lies in Ethan's bed. She gets up and finds a note from John stating that he won't give up on Ethan or their marriage. John has gone off to the lab. He finds Julie, who tells him that the government wants to commission the Humanichs for defense purposes under a quick timeline, requiring that John's protocol by skipped. John puts up a fight, but Julie insists that it is better for them to work on it rather than strangers. John storms out and Julie calls someone, saying that she really screwed up.
Back at their house, Molly declines John's calls and burns John's note. John repeatedly calls Molly from his self-driving car. The car stops on the train tracks as though programmed to do so. His car door refuses to open or start, and John is presumably hit by a train (though we don't see his actual death).
We flash forward again: it is established as six months after John's death. Mental health personnel evaluate Molly, listing out her erratic behavior since her husband's death, including burning down her house, drunk driving, and attacking Julie with a shovel when Julie showed up at John's funeral. Molly becomes abrasive and angry, convinced the government wants to shut her up, and the mental health board tells Molly that she is remaining in custody rather than being released for re-entry. She is taken away by facility workers, to remain in their custody.
We meet JD, a sort of bounty hunter for homicide cases. He is about to have sex when he's interrupted by a criminal activity alert: a dead woman has been found by her landlord, and there is a $20,000 reward for apprehension of the criminal. He refuses a partner on the case, preferring to work alone as usual. He reschedules the sex for Friday and departs to check out the crime scene.
Back at the asylum, Molly overhears the facility workers talking about a murder case: the same case that JD is off on. Molly seduces a phone out of the male worker, Dave. She reads about the case details and remembers seeing a similar-looking corpse, where it appeared that something tore its way out of the victim's stomach. She then tases Dave and escapes to go check out the crime scene, stealing Dave's car to get there.
Back at the Humanichs lab, Julie and Charlie are working on upgrading the Humanichs technology. Julie worries about appearing she is in charge. Charlie asks Julie out and Julie turns him down, presumably for the millionth time.
At the crime scene, she encounters JD. They banter and vaguely flirt, and she tries to convince him that she's the crime scene clean-up service. He doesn't buy it, and scans her, finding out who she is and that she should be at the "rest facility." She tries to explain her theory, that the woman was pregnant and that similar cases have occurred. The mental health workers show up and take Molly back to Restwell. JD continues searching for clues and finds prenatal vitamins in the victim's drawer.
Julie gets home, where Ethan is waiting for her. Ethan wants to know when he can go home and Julie tells him he already is home. Ethan does not seem thrilled about that.
Back at Restwell, Dave attacks Molly (sexually) for ruining his chance at a raise before they're interrupted by another worker who tells Molly she has a visitor. The visitor is JD, who presents a court order releasing Molly as a witness in homicide. They depart to solve the crime in JD's beat-up old Jeep -- only after Molly takes a shovel to the windshield of Dave's car.
Meanwhile, elsewhere, a young African-American man approaches a woman at a bar. He suggests they leave together and she gladly agrees. His eyes change, the way Molly's Offspring's did.