Ana Lucia's death and the ?
Eko is chopping wood with his axe on the beach for the church he is building. Ana Lucia (she has just died in the Swan) 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 Swan computer. Eko tells his brother that he was right and asks him for forgiveness. He interrupts: “Your work being done in this place more important than anything!” and “what is done is done.” 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, only the strange markings previously seen are replaced by question marks (the computer keys are also marked with them).
Confessing to Yemi
In the episode "The Cost of Living", Eko sees Yemi a couple of times throughout the episode, as well as the men he killed in Yemi's church.
As Eko lays nearly unconscious in Locke's hut after being mauled by a polar bear, he sees his brother Yemi, holding a lighter. He clicks his lighter, and tells Eko that he must confess.
Later, wandering through the jungle, an axe is thrown at his head, and Eko sees Emeka and his minions. Eko starts to attack the men, and suddenly Emeka has turned to Daniel, kneeling on the ground. This vision occurs immediately after a puff of smoke flew by Eko as he was lying on the ground.
Finally, Eko is outside of the Pearl, and he sees his brother once more, his clothes dirtier than previously. Eko follows him to a clearing, where Eko finally takes the opportunity to confess to the priest. However, instead of confessing, Eko passes every "bad" thing he's done as things that were necessary to survive and keep the people around him safe. Yemi coldly tells him, "You speak to me as if you were my brother". Eko, now confused and angry, asks the vision who it really is. Instead of finding the man who he believed his younger brother, he found the Monster. In fear, Eko starts reciting Psalm 23 and tries in vain to escape the vengeful beast. After being thrashed about against the ground and thrown against the trees, Eko dies. ("The Cost of Living")