At December's apartment, Donald shows the Observer the trigger he needs for the wormhole generator and explains that it has lost its charge. December points out that if the device did work then they would be wiped from existence, but Donald responds by noting that the humans will be wiped out if the device doesn't work. When December points out that Donald and August both lost control when they were "contaminated" by human emotion, Donald insists that destiny can be changed if someone is willing to sacrifice to make it change, and that the humans are worth saving.
As the team drives back to Harvard, Walter calls Anil and makes sure that he and his team are setting up the magnet. Meanwhile, Broyles calls Peter and tells him that he will be joining them. As he goes upstairs to his office from the parkade, Windmark and a team examine his car and use their soundwave amplification devices to pick up the vibrations of Broyles' conversation with Peter from the windshield.
As Broyles prepares to leave, Windmark comes in and asks for a word with him. He tells Broyles that the resistance recovered Michael and that someone on the inside leaked information to them. Windmark suggests that the Dove, the secret resistance leader, is in Fringe Division, but Broyles dismisses his suspicions. He points out that the Observers would have long ago read the Dove's mind and exposed him. Seemingly satisfied, Windmark tells Broyles to remain vigilant, thanks him for his time, and leaves.
Back at the lab, the team finds Donald waiting for them with the assembled wormhole device. They tell the former Observer how Michael abandoned them and Donald insists that the boy had a reason even if they can't understand it. He then explains that the reactor core trigger's energy has decayed, and that without it they can't activate the wormhole generator. Donald tells them that December has traveled to 2609 to get a new trigger and Walter explains their plan to create the wormhole. The liquid-filled cylinders will act as anchor points at either end, and the magnet will stabilize the cylinder that they send through to Oslo in 2167, the point where they plan to change history. Walter has the generators they need stored in his lab and once they create the wormhole, Michael will travel through and convince the scientist who created the Observers that there's a better way. When Astrid wonders how Michael will find the man, Donald vaguely tells them that there will be someone there to guide the boy.
Broyles is on the road and calls to tell the team that he's heading their way. However, he spots the loyalists trailing him and realizes that Windmark knows he's with the resistance. He tells Olivia that he'll drive around and stall as long as he can, and hangs up before she can figure out where he is and send help. Now that they have a time limit--how long Broyles can hold out against Observer interrogation once he's captured--Walter has everyone go to work.
That night, Peter cuts through more of the amber and finds a syringe. Walter comes in and claims that he doesn't know what it is. There is also a tape with Walter's handwriting on it, addressed to Peter. They watch it and the recorded Walter says that he sent Peter a strange letter, a letter that Peter doesn't know about. On the tape, Walter tells Peter that he's living in the future and is fine, but warns that Peter will never see him again. He admits that he cheated fate so that he could be with his son, but now he has to sacrifice himself to give Olivia and Peter their daughter back as well as save humanity.
Once the tape ends, Walter admits that he lied and that he knows the syringe contains an inoculation for time travel. He explains that he will be the one who takes Michael to 2167 and took the inoculation in 2015, leaving the second syringe for someone else in case he was captured or killed. When Peter wonders why they'll be separated, Walter explains that once Michael changes history, he and the boy will become paradoxes and cease to exist after 2015. They will be trapped in 2167 for the rest of their lives. Walter assures Peter that he's giving his son his life back, and a crying Peter hugs his father, who says that Peter is his very favorite thing. Meanwhile, Michael watches them from the shadows.
Olivia and Astrid go to December's apartment to get the trigger. They find an empty case and December dead. Two loyalists are searching the apartment and Olivia kills one and captures the other. She then demands to know where the trigger is.
An Observer goes to Windmark's office and shows him the trigger. He explains that Windmark's plan to maintain a watch on the eleven original Observers proved successful when they overheard December's conversation with Donald. Windmark realizes that the fugitives plan to use the trigger to travel through time and undo the Observer invasion.
Broyles tries to duck his followers by driving into a tunnel and then abandoning his vehicle. However, an Observer quickly teleports in and knocks him out.
Back at the lab, Olivia and Astrid tell the others what happens. When Donald warns them that they can't do anything without the trigger, Olivia goes to Michael, who has been silently watching the entire exchange. She remembers that he smiled at her in the lab when she rescued him and figures that he knows what do next. He simply puts his fingers to his lips in a gesture for silence. Astrid gets an idea and suggests that they use an Observer shipping lane from 2609. The others agree and Astrid hacks the Observer data files. A shipping lane is scheduled to arrive in New York the next morning, but Donald warns them that they'll need an end-dock stabilizer to redirect it to 2167. Peter assures him that they have one, while Anil calls to tell them that the Observers have captured Broyles. The resistance fighter wonders how Broyles' capture affects their plan, and Olivia tells him that they are ready to go... once they get one more thing.
The team starts bringing up Fringe science bioweapons from Walter's hidden cache. As Olivia takes the biohazard canisters out to the car, Walter tells Peter that he'll be okay. While Astrid tells Walter that she has something to show him, Donald asks to talk to Peter privately. Astrid takes Walter into the amber tunnel and shows him Gene the cow, now embedded in amber. She admits that she found him earlier but didn't want to remove him for fear his mooing would give them away. Walter understands and thanks her for showing him his favorite cow, and she tells him that she's positive that they will win and that soon they will be back in their timestream together with no idea of what happened. They share a brief hug and Walter says her name--correctly--and says that it's beautiful.
Windmark comes to see Broyles and tells him that the initial Observer team were all contaminated by human emotions and gave into their feelings. Broyles says that Windmark seems immune to such contamination and the captain assures him that he does feel hate. The resistance leader says that the feeling is mutual and then winces in pain as Windmark begins his telepathic probe.
Later, Peter and Olivia drive to the Observer District. As they wait for to hear from the Resistance, Peter tells his wife that they'll soon reset the timeline and have Etta back. As they kiss, their contact arrives. He gets them inside and takes them to the air conditioning machinery. Once they're there, Peter and Olivia start dumping the bioweapons into the ventilation system.
At the lab, Walter and Donald prepare to go to the shipping lane. However, Donald tells his friend that he took the last inoculation and that he will take Michael to2167. He explains that he told Peter earlier and he approved, but Walter is desperate to sacrifice himself for everything he's done. Donald says that when he first came to the 21st century, he didn't understand his feelings for Michael. However, since he's seen Walter and Peter together, now he understand the concept of familial love and why it's important. He knows that Michael loves him even if he can't communicate with him, and Walter tells him that's what being a father is about. Donald agrees and says that it's also about changing fate... and protecting their children.
Windmark continues probing Broyles' mind and assuring him that he's a friend and that his teammates will understand if he gives away their location. Broyles finally reveals the location of the Harvard lab just as the alarms go out. Windmark goes out into the corridor and sees loyalists and Observers alike dying from the Fringe bioweapons. Some men have parasites emerging from their chest, one is besieged by hallucinatory butterflies, and others have their orifices sealed over with fast-growing scar tissue. When a cloud of the chemicals approaches Windmark, he teleports aside where more Observers are dying.
Peter and Olivia, wearing gas masks, enter the building and split up. While Peter gets the end-dock stabilizer, Olivia finds Broyles and gets him a gas mask.
The rest of the team goes to the street where the Observers are setting up the shipping lane. Olivia and the others arrive and call to tell Anil that they're in position. The resistance fighters drive the truck with the giant magnet through the barricade and the Observers in charge teleport away to summon reinforcements. The loyalists open fire and the Olivia tells Michael to stay in the car. While the resistance fighters provide cover fire, Donald and Walter set up the equipment and activate the wormhole.
Before Donald can go through with Michael, Windmark teleports in and grabs Michael. Peter jumps the Observer but is easily smashed aside. Windmark teleports to Olivia, chokes her, and then casts her aside. As Olivia falls to the ground, Etta's necklace with the bullet falls out of her pocket. Staring at it, she gets up on hands and knees and glares at Windmark, who is going for Michael again. Every light in the city goes out and Olivia channels all of the power, telekinetically slamming a truck into Windmark and reducing him to a bloody smear just as he tries to teleport away. She looks to Michael, who puts his finger to his lips again.
Donald grabs the boy and runs toward the wormhole through the exchange of gunfire. A bullet hits in him the back and he goes down, dead. Michael kneels next to the man who gave him his genetic material and plays the music box that Donald gave him earlier. Walter comes forward and offers his hand to the boy, who takes it and gets up. As they go to the wormhole, Walter looks back at his son, who mouths the words "I love you." After one last look, Walter and Michael enter the wormhole. There's a flare of white light and...
The year is 2015 and Peter and Olivia are in the park with Etta. Peter admits that he'd like to stay there for the rest of his life but Olivia says that they need to get Etta home. As Peter raises his arms to his daughter, she runs toward him... and hugs her father. The Bishops go home and while Olivia gives Etta a bath, Peter checks the mile. He finds an envelope from his father but the only thing inside is a piece of paper with a drawing of a white tulip.