Yorick and Agent 355 arrive in Boston on their motorcycle.

The city is in ruins. They hide their motorcycle.  Yorick ponders what Dr. Mann will be like. He also notices the graffiti and posters decrying the government and President Brown as liars. They see army tanks drive by, warning people to get off the streets. 

At Harvard, there is too much security for them to get in easily. Agent 355 gets Yorick to hide in an alley, gives him a knife, and tells him to stay put. 

Agent 355 returns to Harvard and poses as an Army sergeant in order to gain entry.

Yorick hears gunfire in the distance and picks a lock to get inside a building.

Agent 355 asks some of the soldiers about their plans and about Dr. Mann. One of them tells 355 about their tactics to keep the rioters at bay. 355 asks why Harvard needs the protection -- the soldier replies that Washington has deemed it valuable. Dr. Mann is not on record as being there. When 355 asks about the lab, she is told that it has been destroyed.

The room in which Yorick finds himself appears to be a hideout for protestors -- there is a printing press, posters, rioting supplies. A woman, who has been hiding, asks him what he is doing in there. She asks him if he's a friend, and he drops the knife. Several protestors return after being teargassed. Yorick helps one of them rinse her eyes. 

The woman asks Yorick if he was here for the manhunt in 2013 when the city locked down. She asks him if he has anywhere to go, telling him that her brother and some friends have a hideout in Jamaica Plain, where he could have testosterone and a place to sleep. Yorick removes his mask. He says he is traveling with a friend. She asks about Ampersand, and Yorick tells her he rescued the monkey from a lab. She tells him where to find her brother, and introduces herself as Steph. 

When Agent 355 returns, Yorick is back sitting in the alley, without his knife. She tells him they have to move, quickly. 

In DC, President Brown and her team discuss the return of Regina Oliver. 

Yorick and Agent 355 search Dr. Mann's apartment. There is an empty crib, which surprises 355 as there was no mention of Dr. Mann having a child. Yorick finds many photos of Dr. Mann at the Union Club of Boston, so they decide to head there.

At the Union Club, Yorick attempts to pick the lock, but Agent 355 gets impatient due to approaching gunfire and shoots the lock off. They search the place and find a fire burning upstairs.

Dr. Mann sneaks up on Yorick and stabs him in the shoulder. They fight until Yorick realizes it's Dr. Mann. Agent 355 tells her that they are from the Federal government. Dr. Mann correctly deduces that Yorick has a Y chromosome.

When Yorick explains that Ampersand is also a male, Dr. Mann gets very excited. Agent 355 explains that Dr. Mann has been selected by the President to continue her existing research. Dr. Mann refuses, saying she is going to San Francisco, where there is a lab with the equipment and software she can use to continue her research. 

Agent 355 stitches up Yorick's wound while Dr. Mann tries to get on Ampersand's good side. 355 says she'll need to inform President Brown about the change of plans. Dr. Mann suggests the President could send a plane, but 355 says Yorick's existence is classified. 355 refers to the rioters as 'crazies' and Dr. Mann defends them, saying the US Government is constantly lying to the populus. 

Agent 355 breaks the satellite phone's anttena and tells Yorick she has to go repair it. She says she'll be back in a few hours, leaving Yorick with Dr. Mann. 

In DC, President Brown's team informs her about the new factions popping up across the country, circulating newsletters with misinformation and conspiracy theories. General Reed informs President Brown that they have located the stolen helicopters -- one has definitely crashed, possibly two, and there is no chance of survivors. President Brown whispers something inaudibly to Christine.

In the washroom, Kimberly accidentally knocks over her purse and it spills toys and crayons everywhere. As she cleans it up, Christine enters and walks past the mess into a stall. Kimberly remarks that President Brown is clearly hiding something about the pilots and helicopters, suggesting they were sent to look for Hero.

Kimberly suggests that it could be bad for Christine if she knew about this. Christine responds shakily, and Kimberly notices that Christine is wiping blood off the floor. Concerned, Kimberly enters the stall and Christine says she is having a miscarriage. Kimberly helps her get cleaned up.

Christine gets an ultrasound, with Kimberly there. Christine asks Kimberly not to tell anyone. The doctor informs them that the fetus is still alive, she's twelve weeks along, and is most likely a girl. Together, the three women listen to the heartbeat.

In Massachusetts, Agent 355 arrives at the address from the note she found in Y: The Last Man Season 1 Episode 2. There, she meets Agent 525. They fight until they realize they are both looking for the same person -- their original recruiter, Fran.

525 tells 355 that it was her first day on the job at the State Department when the Event occurred. 355 tells her the same thing happened to her, only she was sent to the Pentagon. 

525 shares some ammunition and supplies that she has found in her three weeks at the house. She says that Fran doesn't have a tracer -- that she doesn't want to be found. 525 says she will find her and kill her.

Dr. Mann changes her shirt. While Yorick looks away, he notices she has drawn penises on many of the portraits of old white men hanging in the club. Dr. Mann explains that she doesn't enjoy teaching, but she'd rather do it than work for the government. Yorick tells her that he is a magic teacher. 

Dr. Mann asks Yorick about 355. Yorick asks Dr. Mann about San Francisco, inquiring whether it's just the lab she's after or if there is someone special. She tells him that she is gay. 

President Brown prepares to meet Regina, trying to compose herself at the idea of Yorick's death. Christine arrives and informs her that they have identified the bodies of the two pilots, but no sign of Yorick. President Brown has second thoughts about Agent 355's intentions, wondering if she might have killed the pilots on her behalf. Christine says she'll get 355's hard drives decrypted so they can get to the bottom of it. 

Regina Oliver arrives in a wheelchair with an army entourage. President Brown greets her with applause. Christine passes Kimberly in the hallway and gives her a smile, but says nothing.

Kimberly pays Regina a visit. Kimberly tells Regina they must stick together despite past differences, assuring Regina that she "has friends here." President Brown arrives and Kimberly leaves. President Brown tells Regina that they are all working together here, but Regina suggests that President Brown wants to maintain the top position. Regina then asks for some food.

Dr. Mann and Yorick have a conversation about how varied the gender spectrum is. Dr. Mann cites examples of androgynous and intersex people with Y chromosomes, as well as female-identifying people who died during the Event. Yorick mentions the crib, but Dr. Mann insists she has no child. He says she seems sad, and she cites the state of the world as the reason for her sadness -- the insurmountable loss of humanity and biodiversity.

Agent 355 returns, saying they are authorized by the President to head to San Francisco. 355 has kept a tracer.