Eko is unconscious and dreams about when he and his brother, Yemi, were kids. They broke into the church pantry to steal food and were caught. He is told hunger is no excuse to sin and forced to confess. He snaps awake to find Yemi is standing in his tent. Dressed in his priest's collar, he tells Eko to confess his sins and be judged.
Ben brings Jack to Colleen's funeral. Jack asks about the X-rays and guesses that Ben has the tumor. Ben denies it. He then confronts Juliet about it, but she didn't tell Jack.
Sayid, Jin and Sun return to camp, and Sayid updates Locke. Locke proposes they go to the Pearl station and use its computer to contact the Others. He hopes to start a dialogue with them to get back Jack, Kate and Sawyer. Eko mumbled Yemi's name before he disappeared, so Locke believes Eko is going to the Nigerian plane where Yemi's body rests. The plane also happens to be on top of the entrance to the Pearl station.
[break]Back in Nigeria, after Yemi is killed, Eko is returned to the church. Eko walks through it, very aware he was responsible for his brother's death. He finds Yemi's Bible and a photo of them as kids tucked between its pages. He is interrupted by Amina, who asks about Father Yemi. Eko tells her he is taking Yemi's place. Amina introduces her son, Daniel, who is an altar boy in the church.
Outside, they hear gun shots. It's Emeka and his gang who demand the vaccine. Amina tells them it'll arrive on Friday. She explains that the clinic gets ten percent of the vaccine, and Emeka and his gang get the rest as payment for protection. Eko isn't afraid of Emeka, so Emeka shoots and kills a random woman. Eko is angry but keeps quiet so he doesn't blow his cover. Emeka promises to return for the vaccine.
On the island, Eko stumbles through the jungle, dehydrated and delirious. He sees Emeka and his men, bloody and butchered. Then he sees Daniel, who tells him to confess. He stumbles to a stream for water. While he's drinking, he hears the smoke monster and sees its reflection looming menacingly behind him. But then it dissipates, and Locke, Desmond, Sayid, Nikki and Paulo break through the jungle on the opposite side of the stream. Together they continue to the plane and Pearl station.
[break]Ben talks to Jack and tells him they had a wonderful plan to break him. But the plan was ruined when Jack saw Ben's X-rays and figured out he was dying. Ben asks Jack to save his life. Then he asks Jack if he believes in God. Two days after he found out he had a tumor on his spine, a spinal surgeon fell out of the sky. If that isn't proof of God, Ben doesn't know what is.
Flashback to Nigeria, where Eko plans to take the vaccine for himself and sell it. Emeka and his men return after hearing about Eko's plans. Believing Eko really is a priest, Emeka says he'll only cut off Eko's hands. But Eko the war lord emerges, and he slaughters the men inside the church.
Daniel asks if Eko is a bad man. Eko tells him only God knows. Amina confronts Eko about the vaccine, telling him Emeka and his men will simply be replaced by similar men. Eko notices they are boarding up the church. Amina tells Eko it is no longer sacred. He needs to repent because he owes God for every life he's taken, and he owes Father Yemi one church.
In the Hydra station, Juliet shows Jack a movie. While the movie is playing, she apologizes to Jack for what they've done to him, and tries to convince him to perform the operation on Ben. However, the "movie" is actually Juliet holding cards that read the opposite of what she's saying: Ben is dangerous; people want a change; Jack could make Ben's death look like an accident during surgery; she would protect him. Jack is stunned.
[break]In the Pearl station, Sayid concludes they can't send a message to the Others. They check the monitors for other stations on the island, and most of them are blank. But then a live feed reveals another working station on the island when suddenly a face pops into view: a menacing man with a patch over his right eye. He reaches up and turns the camera off. Everyone reacts.
Outside, Yemi appears to Eko asks him if he's ready to confess his sins. Eko refuses to do so. He maintains he has not sinned. He killed to save their lives. He is not sorry he is proud. He asks what has God done for him.
Yemi chastises Eko for speaking to him as if they he were brothers. Suddenly the smoke monster coils up before him. It grabs Eko, and slams him violently against the trees. Locke hears the smoke monster's roar and runs out. By the time he gets to Eko, he is dying. Locke tries to comfort him, but Eko whispers one last thing to him before he dies: they're next.