This episode mainly revolves around Sayid. There is a flash forward where he is shown to be a killer/assassin. He mentions that he is one of the "Oceanic 6" again. This strikes fear into his target. The exact reason for provoking this response, the reason for his selection as a target or his identity/involvement with the story are not given. Sayid then seduces a blonde woman, Elsa. If you pay particular attention you will notice the woman is wearing the same silver bracelet that Naomi had on when Sayid removed it from her corpse.
Frank says that he will fly 3 people to the ship if they can get Charlotte back from Locke safe and well. Sayid, Kate and Miles go to find Locke and retrieve Charlotte. Jack doesn't trust Locke, but knows that he won't kill Kate with Sawyer there.
Dan begins doing some type of science experiment when we learn the names of two more people on the ship; Regina (who will assist in Dan's experiment) and a "McCowski" who is obviously in charge and some sort of tough/strict person. The experiment involves launching a "payload" to the beacon that Dan has set up. They track the payload to the beacon, but nothing arrives. It eventually arrives 31 minutes later.
Sayid, Miles and Kate are taken captive by Locke using Hurley as a decoy at the Barracks. More importantly, Sayid discovers a secret bunker in Ben's House that contains numerous suits, currencies and passports. Sayid asks for Charlotte, and in return he offers Kate and Miles.
Flash forward to assassin Sayid. He is in bed with Elsa and her pager goes off, meaning her boss wants to see her immediately. Sayid immediately tells her not to go, and to run away, as her boss is his target apparently. She tricks him and shoots him in the shoulder. She contacts her boss and warns him. Sayid quickly shoots and kills her.
Desmond is grilling Frank about Penny, since Naomi had the photo of him and her when they discovered her. Frank and Dan look at each other like they know something, but don't say. He says he'll go to the ship with Jack to find out what's happening.
Dan instructs Frank to ensure that he follows "the exact same bearing as when you came in."
Flash forward to a wounded Sayid entering a veterinary clinic. He speaks to someone that is tending to his wound and asks about killing the woman. We learn that this is Ben and Ben is Sayid's boss. Ben is ordering him to kill certain people in an effort to "protect his friends." He also alludes to a point where he asks Sayid, "Do you remember what they did the last time you listened to your heart instead of your gun?" This is obviously a reference to some serious event that ultimately led Sayid to work for Ben as an assassin.