At Coyote Sands, Peter, Nathan, Noah, and Claire continue to turn up buried skeletons. Peter begins to question what they're doing and Nathan insists Angela knows what she's doing. Claire tells Peter to give Nathan a chance. He goes over to talk to Angela, asking her why they came there when she said they needed to find her sister.
Families are brought to the Coyote Sands Relocation Center. Dr. Chandra Suresh greets Alice and Angela Shaw and guides them all through the facility, assuring them it has all of the modern facilities. Chandra says he's come a long way to help them, and has the parents and children separated. The sisters notice there are armed guards but Chandra insists that they're to protect the relocated families.
Later, it starts to rain and Charles Deveaux, Bobby Bishop, and Daniel Linderman come over to talk to the sisters and flirt with them briefly. Once they go, Alice insists she wants to go home but Angela tells her that they are there to get help for Angela's nightmares. She insists she'll always be there for Alice. As Alice cheers up, the rain stops.
Angela tells Peter that her sister and parents died there, and if they don't settle their differences then history will repeat itself. She and Peter are unaware that someone is watching them from a nearby building.
Angela explains that the government told them that they could cure everyone, but locked them up instead. She's been dreaming that her sister is alive even though that isn't possible, and believes that she needs to put her sister's body to rest. Peter wonders why she didn't tell them about Coyote Sands, and Angela insists she did it to protect them, and because it was her nightmare, and the nightmare of the others that formed the Company. She and the others made sure to erase the place's existence as best they could. Angela insists she and Noah was trying to fix the current situation, but Claire is skeptical. Angela says that to ensure their secrecy, they'll have to go back to the old methods of killing and wiping memories. Peter and Claire aren't interested in using those methods and Peter flies off. Nathan goes after him.
Angela wakes up in the middle of the night and goes outside. Deveaux, Linderman, and Bishop are outside. Linderman demonstrates his healing ability and Deveaux warns that they're prisoners, and tells Angela to start believing in her powers. Angela tells them not to trust Suresh, and then goes to Alice when she comes outside to see what's going on. Inside, Alice complains about how her feet are cold. She remembers getting mad when their parents withheld dessert from her, and a hailstorm smashed the car. She believes that she can control the weather, then demonstrates by making it snow outside in the desert. Alice wonders if Suresh will come for her.
Claire tells Angela that she wants to help her. Angela compliments her on her strength and then asks if she's ever done anything terrible. A sandstorm picks up and Angela believes that Alice is responsible. She runs out into the storm and calls out her sister's name, and Claire gets her back inside.
Nathan follows Peter to a nearby café. He says they need to get through things together. Peter points out that Nathan went off on his own, and talks about the time that Nathan convinced him to settle for playoff tickets for a Met games. He says he's trying to find a way to forgive Nathan. They're interrupted when a severe storm warning is broadcast on the television.
Noah is wandering through the sandstorm when debris slams into him, thrown by Mohinder. Mohinder drags him inside and Noah explains that he was working from the inside but was betrayed. Mohinder shows Noah his father's files and explains that he came to Coyote Sands to discover what happened there.
Chandra asks to talk to Angela in private. Alice watches out the window as Chandra takes Angela to his office. He has her demonstrate her abilities as government men tape everything. Angela explains that she had a precognitive dream of their encounter, and she had a dream that Chandra would kill everyone there. Chandra says he would never do that, but Angela warns it will get out of his control. He says that her dreams are subject to misinterpretation, and then prepares to give her an injection.
Angela tells Claire that Alice is alive and the storm is her fault, and she's angry. Angela goes out on her own and Claire follows, but the storm clears and Angela is gone. When Nathan and Peter return, she tells them what happened.
As they search, Mohinder insists his father was a good man but Noah warns him not to make any assumptions. They split up to search for Angela. Peter and Mohinder find Chandra's office and admits he's doing the same thing his father did: experimenting on human guinea pigs out of self interested. Peter says he's being too hard on himself and that Mohinder is a good person. Mohinder warns that he's weak and corruptible, and that the first Company was brutal and angry because of how they were born from Coyote Sands. He hopes that Peter can form a new and better Company because he didn't suffer as the original Company members did.
As they search, Noah tells Nathan that Sylar has acquired shapechanging powers. Nathan admits that he's screwed up. Claire finds a copy of Alice in Wonderland and admits she can't remember the last time they had a family night, or read a book together. She explains to Noah that she tried to impress both of them, but she was stupid and blames herself.
Deveaux tells Angela that it's time to go with the others while the soldiers are changing shifts. It's Angela plans, but she is reluctant to involve Alice. Deveaux tells her to lie to keep Alice calm so they can make their escape. Once he leaves, Angela tells Alice she can't come along but she needs to cover for them. As Alice gets scared, a storm starts outside. Angela tells her she had a dream about Alice and assures her she'll be safe there.
Angela wakes up in an old bunker equipped with furniture, food, and books. A figure descends: Alice, weathered by the desert. Angela tries to get through to her without success as Alice puts a record on and listens.
At the local café, Angela tries to call the police but no one believes them. The boys aren't interested in helping her and Deveaux invites her to dance. She accepts his offer and they dance to the music. The cook interrupts to tell them that they don't allow coloreds to dance with whites. Deveaux uses his powers to cause all of the employees and patrons to forget they're there. Angela remembers they need to get socks for Alice. The radio broadcasts a report of a storm.
Angela reaches out to Alice, who tells her that she's alive and isn't going crazy. Alice explains that she found the bunker and has lived there for almost 50 years, stealing what she needed to survive. When Angela wonders why she stayed, Alice says that she remembered Angela telling her she'd be safe as long as she stayed there, and that the world would be safe from her. Angela asks Alice to explain what happened.
Chandra brings Alice to his office and prepares to give her an injection. A storm picks up and a lightning strike takes out one agent. Alice runs outside and Chandra chases after her and tries to calm her down. When he slaps her, Mr. Shaw comes out and fires a blast of concussive energy, knocking Chandra back. A soldier shoots Mr. Shaw and Alice hides beneath Chandra's laboratory, Building 26, while shots and screams ring out.
Angela tells Alice that it's time to come home, and that she has socks for her to keep her feet warm. She admits she lied to Alice, who grows angry and the storm rages. Peter and Mohinder come in. Mohinder tries to calm her down and Alice remembers his father saying the same thing. She blasts Mohinder back with lightning, and Angela tells Peter she has to talk to her. She advances on her sister and tells her that Peter is her son and Alice has a family. Angela begs Alice not to punish them for her mistakes. As the winds die down, Angela tells Alice to say goodbye and come home with them. Alice says no and runs out of the bunker. Angela goes after her but her sister has disappeared.
Later, Mohinder looks out across the graves, buried by the storm. Peter tells him they're unable to find Alice. Mohinder suspects what his father was up to. Peter gives him a film canister with a recording of what Chandra was doing, but Mohinder says it's best if the past stays buried. When Peter invites him along, Mohinder says he's not ready to move on yet and plans to stay.
At the café, Angela watches and remembers.
Angela tells the three boys that people can't know about them, and she had a dream of the future. They're destined to form a Company that will protect people with special abilities, and they'll do whatever they have to.
Nathan comes over to Angela and hands her Alice's copy of Alice in Wonderland. Angela says she won't ever see her sister again. Nathan says she has to let go of the guilt and invites her to join the others: her family. Peter takes her hand and says they're a family, not a company, and they need to go back to their secret lives. As Nathan says he'll head back to Washington to take ownership of his mistakes, they look up at the television. "Nathan" is on the screen, saying that nothing will be the same, and Noah says it's Sylar.