Dawn is breaking over Coyote Sands and Peter has had it with digging up graves. Why is Angela making them do this? Nathan insists Angela will share her reasons in due time, prompting Peter to climb out of the grave he's been unearthing in disgust. Claire catches up to ask Peter to give Nathan a chance. Nathan knows what he's done, and is carrying enough guilt for all of them; he needs their support. Peter scoffs -- Claire has fallen victim to Nathan's charm -- and takes off to talk to his mother.
Peter reminds Angela that she said they were going to find her sister. No one knew Angela even had a sister! Angela flashes back to 1961, when she was 16. Along with 10-year-old sister Alice, the Shaw family arrives at Coyote Sands Relocation Center by bus. Gentle Dr. Chandra Suresh greets the Shaws and gives them a tour of the family-friendly facilities. He escorts Angela and Alice to a dormitory, explaining that their parents will be staying across the quad. When Angela spies armed soldiers, Chandra explains that this is not a prison -- the soldiers are there to protect them.
A thunderstorm brews as the Shaw sisters get settled. Suddenly the door opens to reveal the "official" welcoming committee -- teenaged Charles Deveaux, Daniel Linderman and Bobby Bishop. When Angela points out that boys aren't allowed in the girls bunk, Charles claims that Bobby wanted to tell Angela how beautiful she is. Bobby protests, so Charles smiles and explains they just wanted to say hi and leave a welcome gift of milk and cookies.
Upset at being separated from her parents, Alice wants to go home. As opposed to packing clothes, Alice has only brought toys and books, including her favorite, "Alice in Wonderland." Angela reminds her that they're going to have fun -- it'll be just like camp. This place is going to make Angela's nightmares go away. No more screaming in the middle of the night. What Angela has is genetic, so the whole family needs to deal with it. No matter what, Angela promises to be there for Alice. The rain stops and the sun shines on the sisters as Angela promises everything will be fine.
Angela holds Peter's hand, confessing that her entire family was killed at Coyote Sands. If the Petrellis don't come together as a family and settle their differences, Angela fears that history will repeat itself. Neither Peter nor Angela notices someone watching them from inside the barracks. Angela explains that she has been dreaming that her sister is alive. Sometimes her dreams don't make sense and are open to interpretation, but now she has to be sure that Alice is truly dead, and if so, give her a proper burial.
Angela confesses that the Company was started right here at Coyote Sands with the goal of never letting what happened here happen again. It worked for 50 years as Angela condoned any method to keep their identities secret. The Petrellis can't keep running, so it's time to go back to the old methods. Claiming the Company tore his family apart, Peter refuses to be part of it again and leaves. Nathan flies off after him.
In March of 1961, Angela bolts awake from another nightmare and runs outside, bumping into Charles and the guys. Linderman notices a scar on Angela's leg and heals it with his touch. Charles explains that Coyote Sands is one big science experiment and they're the lab rats. Angela protests -- after all, they haven't done anything wrong like the Communists. When Charles persists, asking Angela what she dreamed about, she tells him not to trust Chandra.
Having overheard snatches of Angela's conversation with Charles, Alice is worried and her feet are cold. Angela comforts Alice, promising to get her some socks. Alice recalls a night when she was mad at her father, and a hail storm smashed his car -- it seems like she can control the weather. As snow flurries outside the window, Alice worries -- is Chandra going to come for her, too?
Claire has a heart to heart with Angela, who wishes she was half as confident as Claire when she was her age, at the time she first came to Coyote Sands. Maybe things would have turned out differently. Claire presses Angela to divulge what happened. Angela claims it was all her fault as a sand storm spontaneously blows open the door. Angela runs outside, screaming for Alice, convinced her sister is still alive.
Nathan finds Peter at the Coyote Sands CafÃ©, and they immediately start bickering. Peter recalls an incident when they were kids, citing an example of how Nathan is always selfish, even in his generosity. Nathan hopes they can both find the capacity for forgiveness as the TV broadcasts a severe storm warning. Back at Coyote Sands, H.R.G. wanders through the storm, looking for Claire. When he's hit on the head with a plank, Mohinder emerges from the sand clouds to drag H.R.G. to safety.
Mohinder demands to know how H.R.G. found him. H.R.G. claims that he and Angela were trying to stop Danko from the inside, but he found out. Angela brought them to Coyote Sands to uncover the mass graves. And by the way, what is Mohinder doing here? Mohinder admits that his father worked as a doctor on Project Icarus 50 years ago, and produces his files. Back in 1961, Alice looks worried as Chandra takes Angela away for testing.
In Coyote Sands' Laboratory 26, Chandra holds up cards with shapes for Angela to identify. Angela admits that she's not reading Chandra's mind, but she dreamed about this exact moment. She also dreamt that Chandra would kill her family. Promising nothing bad will happen, Chandra pulls out a syringe and prepares to inject Angela. Back in the present, Peter and Nathan return to find Claire looking for Angela, who has disappeared into the storm.
Depressed, Mohinder thinks his father may have been some sort of Dr. Mengele, but H.R.G. reminds him that working with the enemy doesn't necessarily make you the enemy. Chandra was a good man, and they shouldn't make any assumptions until they learn the truth. The guys split up to search for Angela. Peter and Suresh explore Laboratory 26. Mohinder wonders if they're doomed to repeat the mistakes of their parents. His father's work wasn't about science, but self-interest. Peter allows that everyone is selfish.... and his mother wants to re-start the Company. Mohinder hangs on to hope for redemption, even for Nathan.
H.R.G., Nathan and Claire explore the barracks, where Claire finds the book jacket for Alice's copy of "Alice in Wonderland." Claire can't remember the last time she read a book, or enjoyed a simple pleasure. She should be a basketcase after digging up graves, but she's not. She was so busy trying to impress her two fathers and become an agent, when all she really wanted to do was to grow up. Strangely, her dreams of growing up never included becoming an agent.
Back in May of 1961, Alice watches from bed as Angela and Charles whisper at the door. The guys are sneaking out tonight; it's their best chance of saving everyone. Angela balks, but Charles reminds her that it's her plan and they need her. When Angela cites her promise never to leave Alice alone, Charles prompts her to lie. Angela tells Alice that she's going out with the boys because she wants to hang out with kids her own age for once. As thunder breaks overhead, Angela promises Alice that she'll be safe as long as she stays put.
Angela finds herself in an underground storage bunker, where someone has obviously been living. The wind picks up as Alice appears, looking slightly crazy. Remaining silent, Alice plays a record of Roy Orbison's "Crying," which takes Angela back to 1961, when the same song played in the Coyote Sands CafÃ©. Angela tells the guys that she dreamt that they started a Company, dedicated to keeping their secret safe by any means necessary.
Angela gets angry, thinking the guys aren't taking her seriously, but they're enjoying their first moment of simple pleasure in a long time. When Charles realizes that Angela's favorite song is playing, he takes her hand for a dance. The cook interrupts; they don't allow dancing with the colored. Charles pushes that thought right out of the cook's mind and gets back to dancing. With his ability, there's no reason to be afraid. Angela is just remembering she needs to get socks for Alice when an emergency storm warning is broadcast over the radio.
Angela reaches out to touch Alice, who shudders away, clearly having felt the effects of 50 years of living alone. Alice stayed put like Angela told her to. When Angela left that fateful night, Chandra tried to inject Alice. Suddenly a fierce storm started, and lightning struck Chandra's assistant. Alice ran out and Chandra followed, slapping Alice in an attempt to calm her. Alice's father appeared to floor Chandra with a bolt of lightning, and that's when the shooting began. Alice rode out the storm and the extermination, hiding under the barracks.
Angela offers to take Alice home, where she has plenty of socks. For the last 50 years, whenever Angela feels lost, she steals socks for Alice to remind herself that there are simple ways to protect the ones we love. Angela apologizes for lying, infuriating Alice, who kicks another storm into gear. Peter and Mohinder run in as Angela is nearly sizzled by a bolt of lightning. Alice thinks she recognizes Chandra in Mohinder. The wind whips Mohinder against a wall, knocking him out. Alice walks off into the storm ignoring Angela's pleas to stay. Angela tries to follow her, but Alice is gone.
The storms have re-covered all the graves, and the Petrelli family prepares to move out. Mohinder isn't ready to leave yet, so Peter hands him a canister of film he found in the lab and offers a handshake. Angela flashed back to the night she started the Company at the Coyote Sands CafÃ©, then returns to the present to behold her family eating silently. Grieving that she'll never see Alice again, Angela is reluctant to join in, but Nathan advises her to let go of the guilt and join the family for dinner.
Claire breaks the silence asking someone to say something. Peter takes a stand: this isn't a Company, it's a family, and families have the capacity for forgiveness. They're stronger together than they are apart, and it's time to get their lives back. Claire smiles -- what's next? Nathan figures it's time for him to return to D.C. to talk to the President and take ownership of his mistakes. But according to a TV news report, Nathan already is in D.C.! Could it be... Sylar?!