Donald shows December the trigger that he needs for his initiating reaction and explains that it has lost its charge. Without it, the time travel device won't work. When December points out that they will cease to exist if his plan works, Donald points out that humans will ceases to exist if his plan doesn't work. December points out that the twelve of them agreed not to say anything when they developed emotive responses. However, Donald and August lost control, giving themselves away. December says that it's the destiny of the people of that era but Donald insists that destiny can be changed if someone has the will to change it no matter the cost. He tells his associate that he believe the people of the era are worth saving.
As the team drives, Walter manages to call Anil and tell him how to set up the super-magnet they acquired. Meanwhile, Broyles calls Peter and says that he needs to get a few things and then he'll meet them. As he goes upstairs to his office, Windmark and one of his men enter the parking garage behind him and scan Broyles' car
In his office, Broyles downloads his files and gets his belongings.
Windmark's team picks up the sound waves from the windshield and confirms that Broyles spoke to Peter, and that they have Michael.
Broyles' secretary Carol gives him a file with checkpoints on it. Before he can go, Windmark comes in and asks for a word with him. He informs Broyles about Michael's abduction and that someone on the inside helped them. Windmark suggests that the Dove, the secret resistance leader, may be involved. When Broyles points out that if that were the case, he would have been read and exposed long ago, Windmark gets up and leaves, telling him to remain vigilant.
The team returns to the lab with Michael and finds Donald waiting for them. They talk and Olivia wonders why Michael got off the monorail, and Donald assures them that there must be a reason even if they don't understand it. Walter confirms that the magnet has been paced but Donald says that the reactor core has decayed and he's getting a new one from 2609 with December's help. However, he will need one of the team to help him. Walter explains that the device will create a wormhole and then they can deploy the cylinders with the liquid to act as anchors at both ends. One will be placed at 2167, and the magnet will hold it at the precise axis to reach its destination. They need two generators and Walter confirms that he has them stored in the lab. Michael will then go through the wormhole to 2167 and meet the scientist who creates the Observers. When Astrid wonders how Michael will find the scientist, Donald says that someone will be there to guide him.
Broyles calls to tell the team that he's heading for Boston. Windmark has people following Broyles and monitoring his communication. As he drives, Broyles notices the loyalists following him and realizes that the whole thing is a trap. He tells Olivia that he'll stall as long as he can, refuses to let her help him, and hangs up. Realizing that once the Observers interrogate Broyles, they'll know where to find them, Walter says that they need to get to work.
Peter continues cutting through the amber to get to the equipment they need. He finds a syringe but Walter has no idea why he left it there. Next, Peter finds a tape addressed to him in Walter's handwriting. He watches it with Walter and on it, Walter says that he sent Peter an odd letter. He assures Peter that he's fine and living many years into the future, but warns that Peter will never see him again. Peter and Walter watch as the recorded Walter says that he cheated fate so that they could be together, but now he has to sacrifice himself for the sake of Olivia, and Etta, and for humanity.
Once the tape ends, Walter tells Peter that the syringe contains an inoculation for time travel. He will take Michael into the future and left the syringe in case something happened to him and someone else had to do it. When Peter wonders if it has to be that way, Walter explains that he and Michael will disappear after 2015 because they are paradoxes. They will have to live out the rest of their lives in 2167, and Walter tells Peter that he is giving him his life back. Peter hugs his father, crying, and an equal tearful Walter says that Peter is his very favorite thing. Meanwhile, Michael watches the two of them together.
Olivia and Astrid go to December's apartment and find loyalists searching the place. They also find December, dead. Olivia kills one loyalist and captures the other, and demands to know where the reactor part can be found.
An Observer takes the part to Windmark and informs him that his plan to monitor the original Observer team was successful. They realize it will let the fugitives trigger a wormhole and reset time.
That evening, Broyles ditches his car in a tunnel, gets out, and enters a service tunnel. Windmark watches his team's efforts and realizes that Broyles knows that they know. An Observer teleports in and easily captures Broyles.
Olivia and Astrid return to the lab and tell the others about the missing part. Donald warns them that without the part they can't initiate the wormhole. Olivia turns to Michael, realizing he was expecting her on the Other Side, and asks what they should do next. He puts his finger to his lips, and Astrid suggests that they use an Observer shipping lane. Donald and Walter agree and Astrid hacks the coordinates of the next shipping lane. It will open in New York City the next morning at 6:08 a.m. They need an end-dock stabilizer so they can redirect it. Meanwhile, Anil calls to tell them that Broyles has been captured. When he asks how it affects the plan, Olivia says that the plan is a go but they need one thing.
As the team removes the bioweapons from the underground, As Olivia goes to load the car, Walter assures Peter that he'll be okay. Astrid takes Walter to show him something and Donald tells Peter that there's something he needs to say.
Astrid takes Walter into the amber tunnel and shows him Gene the cow, frozen in the amber. She couldn't release the cow because it would moo and give them away, but she figured Walter would want to see her. He admits that Astrid has always known how to soothe him, and she insists that that they'll win and things will go back to normal with no memory that anything ever happened. As Astrid starts to leave, Walter tells her that she has a beautiful name and says it correctly.
Windmark visits the captive Broyles and explains that each of the first twelve Observers that came to that time fell victim to human emotions. When Broyles points out that Windmark seems impervious to any emotions, Windmark admits that he feels something as well: hate. Broyles assures him that the feeling is mutual and Windmark begins probing his mind.
As they wait in the car outside the Observer District, Peter tells Olivia that things are coming to a head and they will soon have Etta back. As they kiss, their resistance contact arrives and takes them inside to the air conditioning room. Olivia and Peter spread the bioweapon chemicals into the air.
At the lab, Walter and Donald prepare to go. Donald tells Walter that he gave himself the last inoculation and that he will take Michael into the future. The former Observer says that he told Peter, and Walter insists that he needs to pay for his arrogance. However, Donald says that since he's seen Peter and Walter together, he's realized what his feelings for Michael and why they're important. He can't communicate with his son, but he knows that Michael will know that he loves him. Walter tells his friend that is what is being a father, and Donald says that it's about changing fate and protecting their children.
Windmark tells the battered Broyles to think about where his friends are. Broyles finally breaks and Windmark realizes that they're at Harvard... and the alarms go off. He goes outside and finds parasites emerging from the bodies of the soldiers due to the biopowder in the air. Windmark evacuates before the gas can reach him and appears in the lobby.
Olivia and Peter, wearing gas masks, enter the building past loyalists and Observers suffering from all the various Fringe science bioweapons in the air. Olivia gets to the monitor room and finds Broyles. She finds Peter, who is taking an end-dock stabilizer, and they go to Broyles and give him a gas mask so he can leave with them.
The rest of the team is near the coordinates for the shipping lane. Olivia calls to tell them that they have the cube and Broyles. Meanwhile, the Observes begin setting up the shipping lane.
Peter, Olivia, and Broyles pull up and inform Anil that they're in position. The resistance fighters drive through the barricades with the truck holding the magnet. As the Observers teleport out, the two sides exchange fire and Olivia tells Michael to stay in the car. Meanwhile, Donald and Walter set up the equipment for the wormhole and Donald activates the end-dock stabilizer, opening the wormhole.
Windmark arrives and yanks Michael out of the car. Peter leaps at the Observer... and they both teleport away. The captain quickly beats Peter and one of his men teleports in and shoots Peter. Olivia and Astrid attack and Windmark grabs Olivia and chokes her, and then throws her to the ground. Etta's necklace falls out of her pocket and she starts to get up as Windmark advances on the boy. All of the power in the city goes dead and Olivia telekinetically slams a car into Windmark, crushing him just as he tries to teleport away.
Michael holds his finger to his lips again and Donald grabs his "son" and takes him to the wormhole, ducking the gunfire from both sides. However, a stray shot hits Donald, killing him. Michael kneels next to Donald and takes out the music box that his father gave him. As he turns the handle, playing Greensleeves
, Walter steps forward and offers the boy his hand. The boy takes it and Walter looks back toward Peter. Peter whispers that he loves him and then Walter and Michael enter the wormhole together.
In the year 2015, Peter and Olivia are in the park together with a young Etta. Peter says that he'd be happy to stay there the rest of his life but Olivia figures that they should head home. Etta runs to her parents... and into her father's loving arms. The family drives home and Peter finds a letter addressed to him from his father. He opens it and finds a drawing of a white tulip.