We start where we ended last season's finale Jack and Kate behind LAX, and this time we get to see the rest of it. Kate drives off, just like we saw her do in last year's finale, but Jack keeps yelling they have to go back. Kate suddenly stops and confronts Jack. She is mad at him for expecting her to care about Jeremy Bentham, the man from the obit. He was crazy, and she's shocked that Jack believed him. She's spent the last three years trying to forget all the horrible things that happened on the day they left how dare he ask her to go back.
On the island Jack and Sawyer race to the Orchid station and run into Hurley. Hurley leads them inside, where Jack comes face-to-face with Locke for the first time since the camp split in two. Locke explains that there's a DHARMA station underneath the greenhouse, but Jack doesn't want to listen. He tells Sawyer and Hurley they'll go back to the helicopter and use it to get all their people off the island. But Hurley tells Jack that might not be the best idea. Keamy and the mercenary team are already on their way back to the helicopter with Ben.
On the freighter, Desmond, Michael and Jin try to figure out what to do about the bomb in the armory. Desmond knows a little about bombs from his army experience. He explains that the radio receiver is like a walkie talkie. Someone sends a signal, and the bomb is triggered remotely. But who has the trigger? Michael realizes it's Keamy. He saw him wiring the remote to his arm. Jin asks if they can turn the bomb off. Desmond says if they disconnect the battery, it triggers the bomb and it explodes. But then Michael gets an idea.
In the jungle, Keamy leads Ben back to the helicopter as Kate bursts out of the jungle. Keamy holds her at gunpoint, and Kate explains she was running away from Ben's people. Instantly, Keamy signals to his men. They take point and search the jungle. From above, an Other jumps out of a tree and garrotes one of Keamy's men. Another lassos a second merc, sending a burst of bullets from his AK-47. Keamy and Omar fire into the jungle, and the Others emerge with guns of their own, firing back. Kate tells Ben to run, and they take off. Keamy tries to shot them, but a grenade lands next to him. He kicks it over to Omar, and KA-BOOM! It explodes, killing Omar.
Keamy runs off after Kate and Ben. They reach the top of an embankment when Sayid leaps out of the jungle and tackles Keamy. They tumble down to the bottom and exchange blows. Then Richard Alpert unloads four shots into Keamy. Kate cuts Ben free, and Ben asks Alpert what their arrangement was. Alpert tells him if they helped free Ben, they would let them leave the island. Ben agrees and lets Kate and Sayid take the helicopter. Kate is shocked he's letting them leave so easily, and Ben simply says that's it.
On the mental institution Hurley gets a visitor. It's Walt. He tells Hurley he waited for someone to come and see him but no one did. Hurley apologizes. But Walt asks Hurley to guess who did visit him. Hurley is surprised to know he visited Walt, too. He told Walt to ask Hurley why all the Oceanic 6 are lying. Hurley tells him it's the only way to protect everyone who didn't come back.
Back in the greenhouse, Locke asks Jack to reconsider staying on the island because he knows he's not supposed to go home. Jack mocks Locke and says right, crashing on the island was their destiny. Locke tells Jack if he leaves, it'll eat him alive until he decides to come back. Jack has had enough and starts to leave, but Locke stops him. Locke tells him they'll have to lie if they leave the island. It's the only way to protect it. Jack says it doesn't need protection. It's just an island. Locke tells him it's a place where miracles happen, but Jack doesn't believe in miracles. Locke tells Jack if he can't believe that, then wait until he sees what he's about to do.
Then Ben comes in. Jack pulls his gun on him, but Ben ignores him. Ben crosses to the planter of anthuriums, bends down and flips the hidden switch underneath. A door next to Ben slides open revealing an elevator. Ben tells Jack that Kate and Sayid are waiting at the helicopter. They better leave and get to the boat within the hour. Locke tells Jack to lie about the island. If he's half as good as he is lying to himself, then everyone will believe him. Locke and Ben get inside and descend below into the Orchid station.
At the beach camp, Faraday returns for the second group to take to the freighter. Faraday tells Charlotte and Miles that they have to be on the next raft out. Miles, surprisingly, doesn't want to leave. He understands the direness of their situation but he wants to stay. Charlotte says she's going to stay for now. Faraday is worried. Charlotte tells him she's still looking for where she was born. She says good-bye and walks off. Faraday leaves with the next group.
At the freighter, Michael lugs in a canister of liquid nitrogen and explains it's to freeze the battery. If the battery is too cold to produce a chemical reaction, then the bomb can't be triggered. It'll buy them some time. Desmond starts a diagram of the wires so they can separate the trip wires. Jin says he'll help, and they start to work.
In the Orchid station, Locke asks what the station was for, and Ben gives him an orientation film to watch. On a monitor, Dr. Edgar Halliwax explains that this is station six of the DHARMA Initiative. It is not a botanical research unit as indicated, and he apologizes for asking them to deceive their family and co-workers. It was done for their own security. The unique properties of the island have created a kind of Casimir effect, allowing them to conduct unique experiments in both space and time. Halliwax indicates an area known as the vault. It was built adjacent to a pocket of what they believe to be negatively charged "exotic matter." Halliwax opens the vault and puts in a rabbit. He explains that care must be taken to avoid leaving inorganic material in the vault chamber, and metallic objects must never be placed inside. In the first demonstration, they will attempt to shift the test subject 100 milliseconds ahead in four-dimensional space. For the briefest of moments, the animal will seem to disappear when in reality-- Halliwax is cut off as the tape locks up and rewinds to the beginning. Locke is alarmed to see Ben putting metal inside the vault. Locke reminds Ben that Halliwax specifically said not to put metal in there. But then they hear the elevator start back up to the greenhouse. Someone called it from up there. Ben asks if he can have his weapon back.
In the freighter, Desmond is about to cut some wires he thinks will deactivate the bomb when Jin suddenly yells out for him to stop. He points out that they lead into another bundle of taped wires that lead into the plastic explosive. There are just too many wires. Michael asks if that means they can't defuse it, and Desmond says he doesn't know. He asks if there's enough liquid nitrogen left, and Michael says he's only got about a quarter of a tank. They better start getting everyone off the ship.
In the Orchid station, the elevator opens and Keamy steps out. The station is empty, but Keamy knows Ben is hiding somewhere and calls out to him, taunting him. He tells Ben he has a dead man's trigger strapped to his arm, which is a heart rate monitor connected to a radio transmitter. If his heart stops beating, it triggers the 500 pounds of C-4 in the freighter and all of Ben's friends explode. Locke steps out from his hiding place and tells Keamy that he and the people on the freighter have no conflict with him. Locke offers to talk about it, but Keamy isn't one for talking. Then Ben burst out of the locker he's hiding in, and with his telescoping baton whacks Keamy over the head multiple times. Keamy goes down, reaching for his knife. Ben grabs the knife first, and in pure, blinding rage, stabs Keamy in the chest. Ben completely snaps, and in a homicidal fury stabs Keamy again, yelling that he killed his daughter. Locke realizes what will happen and tries to pull Ben off him, but it's too late. Keamy is dying.
On the island, Hurley and Sawyer arrive at the helicopter. Kate and Sayid are there, too. Even though things haven't been good between Kate and Sawyer lately, they smile at each other. Jack steps up behind Sawyer, and Kate checks to see how his sutures are doing. Lapidus starts the helicopter, everyone climbs on board, and they lift off. Nervous anticipation and excitement play on their faces. They now have hope they'll finally get off the island. But the chopper soon starts to sputter. Lapidus checks the fuel gauge, and it's quickly decreasing. They look out and see a stream of gas leaking from a bullet hole. Lapidus tells them they have to set down, but Jack insists they fly to the freighter. Lapidus tells them they'll have to get rid of every ounce of extra weight, so everyone starts throwing everything out of the chopper. When there's nothing else left, Lapidus says he wishes he had an extra hundred pounds less. Sawyer looks at the others and makes a decision. He leans over to Kate, whispers something in her ear, and then kisses Kate the kind of kiss that stops time. It's nothing short of spectacular. He breaks away and tells Kate to just do it. Then he jumps out of the chopper into the ocean below. He bops up to the surface and watches as the chopper disappears, then he starts swimming for the shore.
On the outside of the mental institute Sayid approaches a man sitting in a car and shoots him in the chest. The man slumps over dead, and Sayid continues inside. He sneaks into Hurley's room and tells Hurley that he has to leave with him. Hurley asks why, and Sayid says Bentham is dead. Hurley is shocked. Sayid tells Hurley he is being watched he just killed a man outside who has been watching Hurley for the last week. Hurley asks if they're going back, and Sayid says no, just someplace safe.
On the chopper, they can't find the freighter. Lapidus says they must have gotten the engines working and are moving towards the island. Then Hurley shouts out there it is behind them. Lapidus breathes a sigh of relief and banks towards the ship.