The first season comes to an end.
The Marcy & David relationship has been replaced by awkward sipping of tea on his couch as he attempts to locate the Marcy he once knew. He realizes quickly that it’s impossible. She doesn't remember their intimacy or the surgery they performed, or even what tea is - since she is quite perplexed by the hot beverage. She also still thinks David is a reporter, as she did back in the premiere, that casual nudity and kissing someone on the lips as a thank you is a completely normal way to show gratitude.
Kat is angry when MacLaren shows up at the gym to beg for forgiveness. She interrogates him once again about his potential affair. But, this time, the FBI agent responds differently. He admits to it and promises that he is now present and smitten and ready to work on rebuilding their marriage. She doesn't react as positively as he hoped she would and this results in him reacting badly when Carly calls him to ask for a favour regarding Jeff. She wants the MacLaren to use his FBI authority to stop Jeff getting custody of her baby boy. MacLaren is in no mood to help, especially since Carly is the reason Kat is angry with him. He tells her to deal with it on her own and ends the call.
Charlotte, the teenager whose host transfer misfired, grabs her head and dies in agony as her consciousness is overwritten. Once the transfer has completed, another traveler in the house, who plays the role of Charlotte's mother, rushes in to console her "daughter" after what she thought was a nightmare. Charlotte uses a sharp pencil to murder her "mother" and then another to kill the remaining family members. Her next target is high school counsellor Grace Day.
This time Charlotte uses a knife. She goes into Grace’s office claiming to be a student and almost succeeds in stabbing Grace but Trevor intervenes. Charlotte disappears down the hall before announcing that she is on a mission, and Trevor needs to seriously back the fuck off. Trevor calls a team meeting at the hideout. When everyone is together he explains what happened at school that day and identifies the rebel as Charlotte, the teenage misfire.
Philip says that he can't see an SOS but that maybe there wasn’t one sent out because there was no one alive to send it. The crew brainstorms about why the director would order Grace Day killed and discuss the possibility that the director wasn't the one instructing Charlotte. Maybe it was something from the "current" version of the future that MacLaren and his team know nothing about. Grace suggests a group called "The Faction". Apparently, in the days to come, there’s also a group of rogue travelers who split from The Director. The Director is an advanced quantum AI program.
The Faction started their own organization which either came before or after a corruption in The Director's software. In order to protect her leader, Grace did something MacLaren and his team knew nothing about. She "reset" the director. As she was the one who programmed him in the first place, she's able to and she did so without anyone's permission. She rebooted the director's OS using a virus while transferring Marcy's consciousness, which means that she had ulterior motives for re-writing the blonde doctor. MacLaren sees it as a betrayal.
The FBI agent doesn't understand why she would want to reset the AI that’s been running every facet of their lives for decades. Grace expects to be thanked for a job well done as The Faction doesn't believe in the grand plan anyway. Before deflecting Helios, these vigilantes were already in the process of abandoning ship and they are capable of brutality. Grace reveals that they were the ones responsible for capturing the travelers and putting them in those cages and interrogating them. They did so to test the travelers' loyalties and to prevent a mission they did not agree with. Grace came to the 21st to stop them.
She reassures them that The Director will come back online more secure than ever and normality will be restored. But, before that happens, Ms. Day needs to get to a more reliable hideout since Charlotte is following her scent. She wants Trevor to take her to Ellis, the elderly traveler and programmer with the farmhouse in the middle of nowhere. She can guarantee her safety because the farmer has taken precautions and she’s less likely to die out there than in the city where travelers could be overwritten by The Faction. When they arrive at the farmhouse, Ellis isn't home. He returns and shows them a truckload of supplies he was picking up, to build a quantum frame device which is all apart of The Director's "contingency plan".
The contingency plan was thought up when The Faction started activities. This quantum frame device would allow the director to send itself to the 21st. He's had teams working on the core elements for months. Ellis has been keeping some secrets from Grace and she's been keeping some from him, mainly that she rebooted the director. When he hears about this very unnecessary rebooting, he criticizes her and scoffs that only she has an ego big enough to make a move like that. He shows them the quantum frame device in his barn.
Back in the city, a confused Marcy discover's Philip's heroin stash in the bathroom and criticizes the addict. He explains that he was only using again in large quantities because she wasn't around to ween him off of it. She limits how much he gets and orders him to not use above it. She uses exactly the same phrase as before.
David calls to say that a man with a gun is in his home and is pointing the gun at his head, and will continue pointing the gun in that direction until Marcy returns. Marcy proves her shooting and aiming abilities when she fires a bullet into the brain of the assassin. She does this through a vent in David's neighbour's apartment. Afterwards, a traumatized David thinks he should call the police, Marcy thinks otherwise. She advises that he leave the corpse, claim ignorance and buy a one way plane ticket to literally anywhere else. David doesn’t listen and dials 911, he is questioned by the authorities.
When Jeff goes to drop off his baby at a sitter’s house, he doesn’t know that Carly is lurking in the shadows of her car. She looks on sadly and Charlotte comes around the other side of the car with a gun as well. Carly gets a glimpse of this image in her rearview mirror and gets in a few good hits but Charlotte is too strong and well armed. just before Charlotte is about to pull the trigger, Jeff appears and shoots her. Carly does not want to stick around for it. She leaps into the driver’s seat of her car and speeds away. Jeff has a dead teenager on his hands and no one around to verify her criminality.
As MacLaren heads to his car in a parking lot, Officer Boyd steps forward with a pistol as well. Boyd informs him that she was ordered to perform this mission via a messenger. The Director told her to kill MacLaren but she stages the shooting and then takes one in the bulletproof vest from MacLaren so he can escape.
He goes to his wife, he locates Kat in a restaurant and tells her to leave the city because he's got some "work" related problems going on and she's in danger. Although they were bickering only earlier that day, she knows that he's serious and worries for his safety. The assassin collective have located the traveler hideout and as bullets begin piercing through the walls of the homebase and MacLaren, Marcy, Philip, and Carly have to run for their lives. They go to Ellis' farmhouse because they're all suspicious of Grace and Ellis and wonder if Trevor is in danger too. While on the road, Philip and Marcy have an intimate talk about how this Marcy is colder than the previous Marcy. She's upset and he shuts up. Carly and MacLaren also talk - about how they can't be intimate anymore.
MacLaren lectures her about how the mission needs to come first and the future needs to be left in the past and they can't complicate things with more melodramatic emotions. Trevor is not pleased to read a text message he receives from the director which orders him to abort the mission. He wonders if Grace is indeed the evil one but she assures him that The Faction is likely behind that order and to ignore it. The director wouldn’t send a text when communicating something that important. They would send a messenger or he would deliver it directly like he did with Ellis. But Grace wants to know if Ellis received that message before the reset because even then the AI was vulnerable to corruption. Ellis doesn’t see a problem with him receiving it at any time but Trevor has a problem with all of it and intends to destroy the quantum frame using an axe. Ellis points a gun and stops him destroying the device
Carly, MacLaren, Philip and Marcy arrive. Carly is curious to know if Ellis was told to assassinate Trevor. She was told to assassinate MacLaren, so naturally she's questioning the texts. The travelers hold their respective weapons on each other. It emerges that in that in the current version of the future Shelter 41 does not collapse and kill thousands of people - because history has been changed.
Shelter 41 is the birthplace of The Faction. The complications continue when Carly points a gun at MacLaren and Trevor moves to chop up the quantum frame device, Ellis accidentally shoots Grace instead of Trevor, but the bullet goes through Grace's chest into Trevor's so they’re both injured. The quantum frame begins to power up, Ellis becomes a messenger and tells the team to abort the mission and destroy the device. Just as he finishes, MacLaren’s partner, FBI agent Forbes, storms into the barn with back-up just as the quantum frame device completes its power-up sequence.