In the year 2015, the Observers finally conquered the Earth and forced most of humanity to bow before them. The “Natives” formed resistance groups against them, but most were quickly crushed. Some humans have turned “Loyalist” and serve the Observers. Fringe Division remains, but now polices Native crimes under the watchful eye of the Observers.
A Fringe agent, Etta, goes to a club where Observers go to relax. One of them grabs a girl, Kitty, and the owner, Rick, attacks the Observer. Loyalist police quickly restrain him and the Observer in charge of Human activities, Captain Windmark, comes over. Rick spits in his face and Windmark casually wipes it away and then concentrates. The owner’s ears begin to bleed but Etta comes up behind him and knocks him out. She tells Windmark that as a native, Rick is her responsibility and apologizes for any inconvenience. Windmark tries to scan her as well and sarcastically notes that she’s always exactly what she seems.
Etta and Kitty get Rick outside and Rick admits that he had to piss off Windmark so that the Observer couldn’t read his mind. He notes that Etta has no such problem and warns that if the Observers find out that there is anyone who can resist their abilities then they’ll kill them immediately. He then takes Etta to a van where he has a large block wrapped in a blanket. Rick shows the contents to Etta and says that no one else knows about what he has or the other two like it. As he starts to tell Etta where she can find the others, a Loyalist sniper kills him. Etta leaves her contact’s body behind and drives the van to a safe spot. She then checks on the contents and confirms that it’s a block of amber... with Walter Bishop inside.
The next day, Etta meets her fellow agent Simon Foster at Fringe Headquarters. She tells Simon that Rick is dead and explains that she had an open order with the owner to obtain any information on the missing Fringe team. Simon tells her to let it go but Etta explains that she has the legendary Walter Bishop and takes her partner to the storage room where he’s keeping him. They realize that he encased himself in Amber and Etta tells Simon that Rick said that the other members of the Fringe team were at the same place where Walter was. Since Rick died before he could tell Etta where to find them, Etta figures that Walter can tell them once they free him from the amber.
Windmark comes to see Broyles, the Native liaison at Fringe Division. The Observer tries to make small talk and then shows Broyles a hologram of Rick. Windmark warns Broyles that he can’t have native-on-native murders under his command and that the number of them is increasing. When Broyles says that he doesn’t have any leads, Windmark warns him that he’ll have to take over if Broyles can’t do his job. Broyles tells him that he’ll handle it and then asks Windmark why he’s stuck supervising human. The Observer merely smiles and says that he likes animals.
Simon experiments with some of the amber and confirms that it can only be rendered gaseous for a second or two. Etta goes to get some old level-two tech and the storage technician warns her that she doesn’t want to be seen working too closely with Simon, and that his Loyalist friends don’t trust the man. Etta refuses to be baited and takes the weapon, a portable crowd control concussion weapon, back to Simon. Simon transmutes the amber for a split second, giving Etta the chance to blast Walter free of the amber. A groggy Walter stares up at Etta and says that she’s pretty, and she tells him that he’s been in the amber for twenty years.
Walter recovers and Simon has some red licorice for him. They explain that Walter and the other members of Fringe found a way to defeat the Observers and show him the blueprints they have of the device. However, Simon and Etta soon realize that Walter is mentally unstable. They check his brain and confirm that his neural pathways were degraded due to exposure to the amber blast.
Etta goes to see a wheelchair-bound Nina Sharp at the Ministry of Science. The Fringe agent has a cover story to explain why she’s there and Nina is careful to guard her thoughts against nearby Observers. They go outside to Nina’s car and Nina is surprised and pleased to see Walter waiting for her. He doesn’t remember Nina and wanders off, and Etta tells her what happened. Nina admits that Walter and the others saved the world but warns Etta that there are always consequences. However, she admits that she does know a way to restore Walter to normal. Walter had left several brain tissue samples with Massive Dynamic and they’re in a vault at the old building in the city proper across the river. However, Nina warns Etta that the tissue decays quickly outside of storage and that the only sample is in the Massive Dynamic building... in the heart of Observer territory.
Etta and Simon go to get transit passes while Walter waits with Nina and casually fixes her defective cybernetic arm. Once the agents have the passes, they pick Walter up and take him to the transit building. When he sees one of the Observers, Walter yells that he’s a monster, drawing the attention of a Loyalist guard. The man checks their papers and confirms that they’re valid, while Walter rants incoherently. Simon claims that Walter is his grandfather and they’re taking him to his wife’s grave. The officer finally lets them pass but warns them that he won’t be so nice next time. Once they get into the city, the trio goes past the Observers swarming the streets and make it to the old Massive Dynamic building. Using a code that Nina has provided, they get inside through the parking garage and enter the abandoned building. However, they inadvertently set off an alarm, notifying Agent Romick at Fringe Headquarters. He notifies Broyles, who calls Windmark.
Simon and Etta remove the brain samples from storage and prepare a formula from them to inject into Walter. Once they drug him unconscious, they give him the injection and wait for the formula to restore Walter’s original brain patterns. As they wait, Simon talks bout how he was in college when the Observers began their purge, and realized that his parents were resistance members that had sent him as far away as they could for Simon’s own good. Etta admits that she can’t even remember what her parents look like because she lost them when she was 4. Walter wakes, back to his normal self and demands to know if the Observers are still on Earth.
An Observer and his squad of Loyalists officers respond to the alarm and find the tracks leading through the parking garage. The Observer tells his men to kill them on sight.
As Walter studies the blueprints of the weapon he planned to use against the Observers, he informs Simon and Etta that there was one friendly Observer. September warned him that in 2609 the Observers polluted Earth and traveled back in time to find a new place to colonize and make their own. Walter confirms that he can recreate the weapon but warns that it will take some time. Etta asks him about the others on his team and Walter seems to recognize her. Before he can ask who she is, they hear the Observer squad enter the building. Realizing that they’re coming, Walter opens a secret panel and orders Simon and Etta to follow him. When the Observer arrives seconds later, he senses the panel and blasts it open with one of the Observer weapons.
Simon and Etta realize that Walter has gone back and go to get him. He’s in a storage room rigging an anti-matter device and takes Simon’s watch to rig a timing device. Once he’s done, Walter orders them to leave and the trio departs. The Observer and his men come in and try to figure out what the device is... just too late.
Walter, Simon, and Etta get out of the building and the scientist informs the agents that he knows where they can find the rest of the team. He casually walks away as the building disintegrates behind them, killing everyone inside. Down in the sewers, Walter leads the agents to his team, also embedded in amber. Walter creates a wand device to free them while Simon asks Etta what Walter found so familiar about her earlier. However, she ignores her partner’s question.
Broyles receives a report from the Loyalist officer at the transition, confirming that Simon was there. The Fringe chief orders Romick to activate Simon’s transponder and then calls Windmark.
Walter prepares the augmentation buffers that Simon created to free him, to free his teammates. Simon comes over and praises Walter, insisting that he’s the figure that they need to lead the insurgents and show that the Natives can fight back. An increasingly surly Walter tells him to stop pontificating and activates the buffers. Once the amber sublimates momentarily, Etta blasts Astrid free before it can resolidify. However, Simon realizes that the equipment has been damaged. While he tries to fix it, Astrid recovers and looks around, and is surprised to see William Bell embedded in the amber. Walter hushes her before she can comment. Meanwhile, Simon realizes that Broyles has activates his tracker and warns Etta that they’re out of time. He gives Etta the sublimation equipment and tells her to activate it on his mark. Etta hesitates but Simon insists and she frees the next person.
Broyles and his squad arrive in the hideout and find Simon... embedded in the amber in the act of pushing someone out. As his men search the area, Broyles finds a half-eaten piece of red licorice on the floor and realizes what it means.
The remaining team escapes on a monorail and Astrid asks Walter why he left Bell behind. He reminds her of what Bell did to Olivia and says that he doesn’t deserve any compassion. However, he assures his assistant that he has what he needs, and shows her Bell’s severed hand, still embedded in a piece of amber.
Etta is looking out the back of the train and fingering her necklace, which has a spent bullet on it. Peter Bishop comes up behind her and says that he’s sorry about Simon. Etta asks if knows her and Peter points out that he has been in the amber for the last 20 years. However, he looks closely at her and realizes that Etta is short for “Henrietta”: the name of his daughter. Peter hugs his and Olivia’s daughter as the monorail continues on into the night.