After the tail section of the plane crashes into the water off the beach, the survivors swim ashore. Mr. Eko pulls a young girl (Emma) out of the water, and Ana Lucia Cortez performs CPR on her, saving her life. Libby helps a man, later to be identified as Donald, by setting his broken leg. A man runs out of the jungle asking for help, saying there's someone alive in the jungle. The man, "Goodwin," brings Ana to Bernard, who is still belted into his airplane seat, stuck up in a tree. Ana coaxes him to grab the tree branch, just before the seat crashes to the ground. Back on the beach, Goodwin, who claims to be in the Peace Corps, builds a signal fire.

That night, three of the adults are taken and Eko kills two of the "Others" with a rock when they try to take him. From that night on, he refuses to speak.

Three survivors die from injuries on the second through fourth day. A survivor who identifies himself as Nathan suggests staying on the beach, and the group does so. On the fifth day, Donald dies from the leg injury and is buried. On the twelfth day, the Others take nine more, including Emma and her brother Zack. Ana manages to kill another one, who is discovered to be carrying an antique United States Army knife and a list of the nine to be taken, along with their descriptions. While trying to sort out what happened, the notion of an infiltrator in their midst is discussed, as well as a proposal to leave the beach.

The survivors opt to head into the jungle. They make a camp near a source of fresh water and fruit trees. Ana digs a pit, which she turns into a cage. As soon as it is done, she knocks Nathan unconscious and throws him into the pit. She interrogates him, believing he is one of those who took the children, due to his unexplained absences and how nobody remembered seeing him on the plane. When asked where he came from, he replies, "Canada." She begins starving him, demanding to know the location of the children, but Mr. Eko feeds him when she is not looking. Ana tells Goodwin she intends to start torturing Nathan the next day. That night, Goodwin frees Nathan, warning him of Ana's plan; when Nathan turns to leave, Goodwin breaks his neck, revealing to the viewers that he is the infiltrator.

The survivors move again and find the bunker marked by a Dharma Initiative logo, with an arrow in the center. Inside a box they find a glass eye, a Bible and a radio. Goodwin and Ana go to higher ground to try to pick up a signal. While there, Ana reveals that she knows Goodwin is one of the Others, because on the first day, he ran out of the jungle with his clothes completely dry, ten minutes after the plane crashed into the water. Goodwin admits he killed Nathan, says that those taken were "good people", and that Nathan was not on the list because he was "not a good person." The two fight for the Army knife; when they roll down a hill, Ana impales him on a sharpened stick.

Ana returns to the survivors and tells them, "We're safe here now". On the forty-first day, Bernard picks up Boone on the radio, and responds to Boone's "We're the survivors of the crash of Oceanic Flight 815" with "We are the survivors of flight 815." Before any further conversation can take place, Ana turns off the radio, dismissing the transmission as another trick by the Others. "They know we were on Flight 815 because Goodwin knew we were on Flight 815," she argues. "This is our life now," she tells them. She goes off by herself to cry, and Eko tells her everything will be all right. She asks him why it took him forty days to speak; he asks her why it took her forty days to cry.

Soon after, Cindy and Libby find Jin washed up on the shore. After pulling him from the water, they tie him up and blindfold him while they try to find out who he is. As Eko and Ana Lucia argue, Jin breaks free and runs to the beach.

The remainder of the episode is shown as a montage of the events already seen in the episodes Orientation through Abandoned, including the tail section's acceptance of Jin, Sawyer and Michael, the trek to the midsection's camp, Sawyer falling ill, Cindy listening to the forest's whispers just before she is "taken", and the shooting of Shannon by Ana Lucia.