Mr. Eko, working as a priest and going by "Father Tunde," visits the confessional, speaking to a man who claimed to have committed adultery, but had really forged an Australian passport for Eko to enter the United States. Another priest comes to inform Eko that a miracle has happened: A woman claimed that her child drowned in a river and resurrected the day after, and she wanted to tell the world the news. Eko declines to be concerned with this matter, as he does not believe the woman, to which the priest responds, "Why do you think I chose you?"
Later, Eko is seen interviewing a medical examiner about his account of the "miracle" that happened. The examiner informs a skeptical Mr. Eko, that the girl was resurrected during the autopsy, and provides an audiotape as supporting evidence. When Eko goes to visit the woman who reported this miracle, he finds a stare-eyed daughter at the porch. The mother comes out and informs him that it is not an appropriate time for him to visit.
The father comes out and orders her to go back inside, and tells Eko that the whole incident was a misunderstanding. He claims that his wife knows that his psychic services are a fraud, and was attempting to "spite" him.
Eko then tells him that he will report that the incident was not a miracle. As he leaves, he sees the daughter staring at him from the window.
Finally, Eko stands at the Oceanic Airlines terminal picking up his tickets for the flight, when the drowned girl confronts him as he steps away from the desk. She informs Eko, to his anger and disbelief, that his brother Yemi has contacted her when she was "between places." She then says she knows that Eko's not a real priest, but he should have faith in himself, as Yemi still has faith in him. Eko's fury causes Libby to overhear their conversation and ask them if everything is all right. Eko shrugs it off and leaves.
On the Island
We see Eko chopping wood with his axe on the beach, continuing to build his church. Ana Lucia shows up, and asks him what he is building. Eko explains and claims that the idea of a church came from a dream. Ana Lucia responds, "A dream like this one?" Eko then notices that Ana Lucia is bleeding from the stomach and out of her mouth. She tells Eko, "You need to help John." Eko then finds himself in the Swan, with his dead brother Yemi sitting at the computer. Yemi tells him that Locke has lost his way, and that Eko needs Locke to take him to "the question mark." He also tells him to bring the axe. The room starts to violently shake. The timer is back at the red and black tiles, but now the hieroglyphs previously seen are replaced by question marks. The computer keys are also marked with them. Eko wakes up hyperventilating, and Charlie, sleeping nearby, turns over and asks, "What's the matter?"
The action then returns to the final events of the previous episode. Locke, Sawyer, Kate, and Jack are seen moving through the forest, as Michael stumbles out of the Hatch, claiming that he had been shot in the arm by a person unknown to him. Eko appears out of nowhere and offers his help. Sawyer discovers that Ana Lucia and Libby have suffered gunshot wounds. Kate checks Ana Lucia for a pulse and tells Jack that she is dead. Libby however coughs up a mouthful of blood, and Jack rushes to treat her. She quickly enters into a state of shock. Fear crosses Michael's face; if Libby lives, she may reveal that it was Michael who shot them. Jack insists that they go after "Henry's" trail, as Michael says he left only half an hour earlier. Sawyer insists that Jack remain and tend to Libby's condition.
Eko offers to track down Henry Gale, with the assistance of Locke. Both of them head out to find him. However, Eko leads Locke on a random path, making no effort to pick up or follow a trail that Henry Gale would have left. Locke is upset and prepares to head back. Eko then asks Locke to take him to the question mark. When Locke refuses, Eko headbutts Locke, successfully knocking him unconscious. When Locke later regains consciousness, Eko tells him that he was being difficult. After further interrogation, Locke shows Eko the diagram he drew from his memories of the blast door, with the question mark in the middle. Eko then tells Locke that they will go to the question mark, stating that Ana Lucia told them in his dream to find it. Locke responds with a look of skepticism, to which Eko asks him, "Have you ever followed a dream?" Later, as the two are arguing about symbols on the map that Locke had copied from memory, Eko steps on a Virgin Mary statue, and the two stumble before the burned plane with the heroin smugglers. Eko asks what made the plane fall and Locke answers that it was "Boone who made it fall". He then ads in a nonchalant tone that it was "a sacrifice that the island demanded." They then make camp and "wait for further instructions."
In the Hatch, Michael asks if Libby had said anything. Jack says that she is still unconscious and is suffering, and that all he can really do is to make her more comfortable. Jack then gives Sawyer a stern look, to which Sawyer says that he already gave him all of the medications. Jack clarifies; he was referring to the heroin. He then asks Sawyer to fetch it, and orders Kate to accompany him so that she may find where Sawyer stowed all the guns and other belongings. Faced with the choice of this or allowing Libby to die in pain, Sawyer agrees and leads Kate back to his tent. Kate learns to her surprise that he hid his belongings underneath the tent. After they walk out of the tent, Hurley approaches them and asks if they seen Libby; their faces fall as they begin to explain.
In a dream, Yemi appears before Eko and directs him to climb the cliff. Upon reaching the top, Yemi, seated in a wheelchair, says "Wake up John", and in terror, Eko loses his grip of the cliff and falls back to the bottom. Locke is shown waking up from a disturbing nightmare. When he begins to describe his dream, Eko tells him that the priest he saw was his brother, Yemi. Locke stated that Yemi wanted him to follow. He then looks up the cliff from his dream, and Eko proceeds to climb the cliff. Half-way through his climb, he is seen struggling, which makes Locke anxious. However, Eko successfully makes it to the top. Locke calls to him and asks him if he has found anything. After looking at a rugged green-covered landscape, Eko replies that he did not find anything. But as he turns to tell Locke, he sees a giant question mark on the ground formed by bare earth, with the plane lying next to it.
After tasting it, Eko discovered that the soil was salted in the pattern of a question mark to prevent growth. Eko then picks the ground with his axe, and discovers a hatch buried underneath the plane. Using the blunt side of the axe as a sledge hammer, they open and enter the Hatch below, which appears to have electrical power. They enter a room with several tables (one with cigarette debris on it) with adjustable rectangular magnifying lenses, as well as several television screens mounted into a wall, one of which Locke turns on: it shows a live surveillance feed from the Swan; Jack is shown walking past the camera. Locke sees another camera above them, and also finds a pneumatic tube which is proven to be functioning when he inserts his map sketch.
Locke also finds another computer terminal with a command prompt: >: PRINT LOG? Y/N. Locke inputs Y, and a dot-matrix printer is heard in the background as it produces the log printout.
Eko finds another Orientation movie on a U-matic tape. Eko and Locke watch the tape and learn that the hatch they are in is "Station 5 - The Pearl," constructed to observe the other station(s) and to record how the subjects perform actions which they believe to be of great importance. Locke appears to be disillusioned about entering the Numbers, whereas Eko's belief in its importance is heightened--he takes the log printout with him as they depart.
Back at the Swan, Hurley says his goodbyes, and tells her how sorry he is for having forgotten the blankets. Jack could not save Libby's life. Her last word was a hoarse "Michael...," which Jack misinterprets as a sign of concern, and not as a sign of warning. When Jack reassures Libby that Michael is fine, she appears to be frightened, and then dies. While Sawyer hugs Kate (who starts crying), Locke and Eko make their way back to camp. Michael stares at the computer from the armory, as the alarm starts beeping.