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I saw someone saying on the comments where is badass Ben Linus this season.
I just re-watched the Man from Tallahassee from Season 3. Ben says to Locke "I wanted to know what it felt like when your own father tried to kill you. He's the reason you destroyed the submarine isn't he? You're afraid. You're afraid of him and this is the one place he can never find you, this is the one place he can never get to you." Locke: "What do you want from me?" Ben: "I don't know how it happened, but you seem to have some communion with this island John, and that makes you very very important. You have no idea what you're talking about of course, but in time you'll have a better understanding. So what do I want? I want to help you John." Then he shows him Anthony Cooper, his father.
Then I re-watched the Brig and Anthony Cooper bites John's hand and Cooper says, "Don't you know John, don't you know where we are?" Eventually, when he's in the black rock with Sawyer he tells Sawyer he thinks we're all in hell and Sawyer chokes him while saying, "you wanna go to hell?"
So Richard, Ben and Miles are walking towards their mission to blow up the plane when Richard and Ben start talking. Ben: "Hey remember that magic box that whatever you wanted to be in there would be in there? Richard: "You mean the one that brought back the man from Tallahassee that you used to keep Locke from being the leader because you're a jerk?" Ben: "Yeah that one. So both Locke and Sawyer were candidates when that happened, and that may be why Cooper showed up in the first place, not just to test Locke, but also Sawyer because he's a candidate." Richard: "Okay, so what's your point?" Well, if the box is supposed to bring people to test our candidates, then maybe we should check it and see if there's anyone else in there.
Miles: "What the hell are you guys going on about?"
Ben: "Slight change of plans, Miles."