The mercenaries arrive back on the freighter, beaten and wounded by the smoke monster and unsuccessful in their mission to capture Ben.
Keamy, their leader, accuses Captain Gault of warning Ben that they were coming. Gault says he wasn't the one. And he leads Keamy below deck, where Michael--outed as Ben's spy--is locked in a room. Keamy wants to kill Michael but Gault stops him, saying that only Michael can fix the ship's engines, since he's the one who disabled them in the first place.
Keamy is determined to go back to the island. In the captain's quarters, he fishes out a folder from a safe. It's a map, provided by Widmore, that shows where Ben "is going" on the island. Keamy plans to go back and "torch" the island in order to drive Ben to that spot.
Gault, however, is very unhappy about this plan. He signed on to capture Ben, not kill people. He later confides in Sayid and Desmond and makes arrangements for them to go back to the island to warn the people there. Desmond elects to stay on the freighter. He's spent too much time on the island already and he's convinced that he'll be able to see Penelope soon if he stays on the ship. He wishes Sayid success and they part.
When Keamy orders Frank to start up the helicopter to fly the mercenaries back to the island, the pilot refuses. Keamy then slashes the doctor's throat and shoots Gault. Knowing that others will be killed unless he follows orders, Frank starts up the chopper.
Back in the jungle, Locke has a vision of Horace, the Dharma Initiative member who, years ago, recruited Ben's father to come to the island. Horace tells Locke "you need to find me" in order to locate Jacob.
Later, Locke brings Hurley and Ben to the mass Dharma grave. He finds Horace's body and fishes something out of the dead man's pocket. It's a map to Jacob's cabin.
In flashbacks, way back to the late 1950s, we see Locke's real mother give birth to him in the hospital after being struck by a car. Locke is premature and his mother is young and unmarried. As she and her own mother visit the baby in his incubator, there's a strange visitor lurking outside the room. It's Richard Alpert, looking the same age as we've seen him many years later on the island.
When Locke is a young boy, Richard visits again. He comes to Locke's foster home saying that he directs a school for special children and he thinks that Locke may be a candidate to go there. Alone with Locke, he places several items on a table. A vial of what looks like sand, a compass, a baseball mitt, a book titled "Book of Law," a comic book and a knife. Richard asks Locke to select the items that belong to him. Locke selects the sand and compass and Richard seems pleased. But when Locke selects the knife, he's disappointed. It seems Locke isn't who Richard was looking for.
We later see a teen-age Locke getting teased and bullied at school. A teacher calls him into his office. Locke is apparently gifted at science and has received an invitation from a Richard Alpert of Mittelos laboratories in Portland to attend a science camp. Locke wants nothing to do with it. Even though it's not really what's he's cut out for, he insists on trying to be a tough guy, into the outdoors and sports and cars. The teacher says Locke shouldn't fight being who is, and Locke says "Don't tell me what I can't do." Needless to say, he doesn't go to science camp.
Years later, after his spine has been crushed, Locke is shown in physical rehabilitation. An orderly who wheels him out of the session is none other than Michael Abbadon, who encourages Locke to go on a walkabout, it will show him what he's truly capable of.
Back on the beach, Jack and the rest see the freighter chopper approach. Something drops out. It's a tracking device showing them where the helicopter is headed, as if somebody wants them to follow.
Back in the jungle again, Locke enters Jacob's cabin alone. He encounters a man sitting in the dark. It's Christian Shepherd. Claire is in the cabin, too. Locke is confused as to what's going on, but Christian says the facts don't matter now--Locke needs to ask a more important question. So Locke asks "How do I save the island?"
Outside, Ben asks Locke what he was told. Locke says, "He wants us to move the island."
* What's up with the confusing, mixed-up timeline involving the doctor's death? Those on the beach discover his body but are told by the freighter crew over the sattelite phone that the doctor is on board and alive and well. We know the doctor is killed by Keamy, but Keamy is on the island searching for Ben at the same time he's supposedly killing the doctor on the ship, i.e. in two places at the same time.
* Ben tells Locke: "I used to have dreams." Why did he stop having such visions? Were they supplied by Jacob, who is now more interested in Locke?
* Ben also indicates that it wasn't his idea to kill the Dharma Initiative members. Was it Jacob's?
* What's the secret to Richard's seemingly eternal youth?
* Richard notices a picture young Locke has drawn. It seems to show somebody being attacked by the smoke monster.
* Locke is shown playing backgammon as a boy. It's a game he later taught Walt how to play on the island.
* Teenage Locke has a Geronimo Jackson poster in his school locker.
* Christian says he isn't Jacob, but can speak for him. Is Jacob somehow making use of Christian's body?
* What about Claire? Is she dead? Christian says Aaron isn't in the cabin. He shouldn't be, indicating that he and Claire are ghosts(?).
* Is Locke Jacob? Could be, given the twists in time involved here, that he becomes Jacob. Alpert knows there's something special about him. The items Alpert shows to Locke may belong to Jacob later in time. Or perhaps Locke is Jacob's reincarnation?
* How the heck is Locke going to move the island? Physically? Interdimensionally? In time?
* Keamy's gun failed when he tried to kill Michael, reinforcing the idea that Michael can't be killed and can't kill himself, although he tried several times. Jacob, or the island, or whatever, wants him alive.
* As mentioned earlier, when Juliet was recruited to work for the company, Mittelos is an anagram for "lost time."