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Season 6, Episode 7: "Dr. Linus"
Fleeing the carnage at the Temple, Ben runs through the jungle, scared and alone until he finally catches up with Ilana, Sun, Miles and Lapidus. He tells them that Sayid won't be joining them on account of having killed Dogen and Lennon, and convinces the group to go back to the survivors' camp.
Dr. Ben Linus, European History teacher, lectures his class about Napoleon's exile to the island of Elba. As the class is dismissed, Linus is summoned by Principal Reynolds  and told that he'll be supervising the after-school detentions all week rather than holding "History Club", an extracurricular study program. Ben is upset, because he wants to help those students that genuinely want to learn, but Reynolds thinks is a waste of time. In the staff room, Ben and Arzt, the science teacher, complain about how Reynolds cares more about the school's budget than the students. Locke, the substitute teacher, plants the idea in Ben's head that maybe he should be the principal.
As Miles asks Ben about the Smoke Monster, Ilana suddenly starts questioning Ben about how Jacob died. She gives Miles the bag of Jacob's ashes, he does a reading and confirms Ilana's suspicions that Ben was the one who killed Jacob. Ben protests his innocence, but no one believes him. After a night of hiking through the jungle, the group returns to the survivors' beach camp and scrounge for supplies while Ilana starts stripping some airplane wreckage for cabling. Ben tries to convince her that Miles isn't trustworthy, but she shrugs him off.
At home, Ben makes dinner for Roger, his sick and elderly father, while wondering out loud if he's a bigger loser than the kids he's babysitting in detention.
Roger: This isn't the life I wanted for you, Ben. I wanted so much more.
Ben: I know.
Roger: That's why I signed up for that damn DHARMA Initiative and took you to the island, and... They were decent people. Smarter than I'll ever be. Imagine how different our lives would have been if we'd stayed.
Ben: Yes, we'd have both lived happily ever after...
Roger: No, I'm serious, Ben! Who knows what you would have become?
They're interrupted by a visitor: Alex Rousseau, one of Ben's History Club students. She's disappointed that History Club has to be cancelled for the week, since she's got a History test and was hoping for the tutoring, so Ben offers to meet her in the library before school and help her out.
As Ilana storms around the camp and picks up odd items, Sun asks her what's going on and finds out about the Candidates, and that Ilana was sent by Jacob to guard the remaining ones. In the jungle, Jack wakes Hurley and they head off towards the Temple. Hurley tries to stall and gives bad directions, remembering Jacob's warning, but they run into Richard and he insists on leading them. At the beach, Ben and Lapidus collect useful items and muse over how long it's been since Oceanic 815 crashed. Ben is very intrigued when Lapidus reveals that he was supposed to have been the pilot but "overslept" and missed the flight.
Lapidus: Can you believe it? Imagine how different my life would be had that alarm gone off.
Ben: How different would it have been? The Island still got you in the end, didn't it?
Just then, Ilana puts a gun to Ben's head, marches him to the survivors' graveyard, tethers him to a tree, gives him a makeshift shovel and orders him to dig his own grave.
Before school, Ben tutors Alex on European history. She's very bright, but extremely stressed out about the upcoming test and how it will affect her future, especially her dream to go to Yale. Ben is nothing but encouraging and offers to write her a great recommendation letter, but Alex says that it would need to come from a Yale graduate, and the only one she knows is Principal Reynolds. When she calls him a "pervert", Ben presses her for more information and learns that Reynolds and the school nurse have been having an affair, even having sex on school property. Ben promises not to tell anyone, but there's a look in his eye that's very reminiscent of the original Benjamin Linus...
Ben digs the grave as Ilana watches. When Miles comes by with some food, Ben reminds him of the attempted blackmail and offers to get Miles the $3.2 million in exchange for helping him escape. Miles refuses, since he can just as easily dig up Nikki and Paulo for the $8 million in diamonds they were buried with.
Ben: I can't believe you're just gonna stand by and watch this happen. Ilana's gonna murder me! For killing Jacob, a man who didn't even care about being killed!
Miles: No, he cared.
Ben: Excuse me?
Miles: Right up until the second the knife went through his heart, he was hoping he was wrong about you. I guess he wasn't.
Richard leads Hurley and Jack through the jungle, while Hurley asks whether Richard's agelessness has anything to do with time travel, cyborgs or vampirism. Richard answers that he was "touched" by Jacob and given the "gift" of immortality, though he considers it more of a curse. They arrive at their destination: not the Temple, but the Black Rock. Richard reveals that everyone at the Temple is dead (though there was no sign of Kate or Sayid) and tells Hurley not to believe anything Jacob says before marching into the Black Rock to "die".
Arzt is marking papers when Ben arrives and asks him to access the school nurse's email account. Ben lays out his scheme to get proof of her affair with Principal Reynolds and use it to blackmail him for the job of school principal. Arzt agrees to help in exchange for a better parking spot and better teaching equipment, and admits he didn't have Ben pegged for such "a real killer".
On the Black Rock, Richard wanders through the hold and tells Jack that he's been to the Black Rock before, but only once. As Hurley follows them in, Richard grabs a stick of dynamite out of a crate and asks Jack to light the fuse on it: part of Richard's "gift" from Jacob is that he cannot kill himself, and if he lit the fuse himself, it simply would not work. Jack lights the fuse on the dynamite, sets it down in front of Richard… and then sits down across from him and says "Let's talk." Hurley freaks out and demands that Jack leave with him, but Jack is confident that nothing will happen. He tells Hurley to leave, and reluctantly, Hurley does so, leaving Jack and Richard alone with the dynamite.
Richard: You're gonna die.
Jack: Actually, I don't think either one of us is gonna die.
Richard: What makes you think that?
Jack: I just came from a lighthouse where my name was etched in wood on a dial. I turned a mirror that somehow reflected the image of the house I grew up in. Jacob's lighthouse. He got Hurley to bring me out there because he wanted me to see what was reflected in that mirror. For some reason, he wanted me to know that he had been watching me ever since I was a kid.
Jack: I have no idea why. But I'm willing to bet you that if Jacob went to that trouble, that he brought me to this island for a reason. And it's not to blow up sitting here with you right now.
Richard: That's a pretty big risk you're taking Jack.
Richard: What if you're wrong?
Jack: I'm not.
At the last moment, the fuse fizzles out and the dynamite doesn't explode. Convinced, Richard defers to Jack's idea of going back "to where we started". At the beach, Ben is still digging when the Man in Black arrives to speak to him, out of sight of Ilana and the others. He tells Ben about his plan to leave the Island, and offers to put Ben in charge of the Island once he's gone. He even gives Ben a chance to escape by freeing him from the tether, leaving a loaded rifle in the jungle and telling Ben to meet him on Hydra Island. Once the Man in Black has left, Ben makes a break for it into the jungle with Ilana hot on his heels.
Ben goes into Principal Reynolds office with copies of the incriminating emails and, in classic Benjamin Linus form, gives him an ultimatum: resign and write a recommendation to the school board that Ben take over the principal job, or else the emails go to the school board--ending his career--and to Reynolds' wife--likely ending his marriage. Reynolds, however, has an ultimatum of his own. He knows that Alex needs a recommendation letter in order to get into Yale, but if Ben goes through with his scheme, Reynolds will write a very scathing letter instead, effectively destroying Alex's future.
In the jungle, Ben finds the rifle left for him by the Man in Black and gets the drop on Ilana. He forces her to drop her gun and surrender, but he doesn't shoot her.
Ilana: What are you waiting for?
Ben: I want to explain.
Ilana: Explain what?
Ben: I want to explain that I know what you're feeling.
Ilana: You have no idea what I'm feeling.
Ben: [tearing up] I watched my daughter, Alex, die in front of me. And it was my fault. I had a chance to save her, but I chose the Island. Over her. All in the name of Jacob. I sacrificed everything for him, and he didn't even care. Yeah, I stabbed him. I was... so angry. Confused. I was terrified that I was about to lose the only thing that had ever mattered to me: my power. But the thing that really mattered was already gone. I'm sorry that I killed Jacob. I am, and I do not expect you to forgive me because... I can never forgive myself.
Ilana: Then what do you want?
Ben: Just let me leave.
Ilana: Where will you go?
Ben: To Locke.
Ben: Because he's the only one who'll have me.
Ilana: I'll have you.
Ilana picks up her gun and walks back to camp. A moment later, Ben follows.
Ben goes into the principal's office. Reynolds isn't there, and Ben briefly toys with the name plaque on the desk when Alex enters. She wants to thank Reynolds for the glowing letter of recommendation he wrote, and wonders if Ben had anything to do with it (he says "no"). When Reynolds arrives, Ben slyly gets him to find someone else to cover detention, and tells Alex the History Club is back on. Outside, Arzt is livid that Ben didn't go through with the scheme and that he won't be getting a new parking space. Ben offers his own space to Arzt and, content, goes off to his next class.
Ilana and Ben return to the camp, and Sun accepts his offer to help her put up a tent. Lapidus builds a fire while Miles sits off on his own, inspecting a bag of diamonds. Ilana sheds a few tears as she mourns for Jacob. As this happens, Jack, Hurley and Richard arrive. The reunion is mostly joyous, but Richard and Ben both stand apart from the group. Observing all this is a submarine periscope, and a young sailor reports what he sees to his boss: Charles Widmore.