Episode 3x19, The Brig
When Locke goes to see Ben in Ben's tent, Ben tells him that Juliet is collecting data so that they can take the pregnant women from the survivors' beach.He shows Locke how he can walk with a cane and says that it's because of Locke that he can walk and soon Locke will be allowed to know the island's secrets. Locke says he's ready now, but Ben says Locke's not ready. First he needs to be free of his father and the only way to be free is for Locke to kill him.
At night, Ben wakes Locke and tells him it's time. He takes him to where Anthony is tied, and, as people gather, tells Locke to kill him. Locke can't do it and Ben apologizes to those standing around, saying that Locke is not the person they'd thought he was.
Episode 3x20, The Man Behind the Curtain
Ben says that he answers to Jacob and Locke insists that Ben take him to see Jacob. Ben says he can't take Locke there, but after Locke announces to everyone that Ben is taking him and beats up Mikhail, Ben takes him.Ben talks to Jacob, but Locke can't see him. Locke shines a flashlight and the room shakes, the door closes, and things fall off shelves. Ben tells him to stop and is thrown against the wall.
Ben wants to know what Jacob said to Locke, but Locke won't tell him. Ben shows him the Dharma grave. Ben shoots Locke and he falls into the grave.
Episode 3x21, Greatest Hits
Ben gets back to his camp and acts nervously when Alex starts asking questions. Richard also asks questions and Ben says that Locke had an accident. He also says that they will go to take the pregnant women tonight instead of tomorrow night.Despite Richard's feelings that moving the schedule up is not a good idea, Ben tells Ryan Pryce to get his men ready and to leave immediately.
Episode 3x22, Through the Looking Glass
Ben gets a call on the walkie-talkie from Bonnie. He asks why she's breaking radio silence and she tells him that one of the crash survivors is in The Looking Glass. He finds out that it's Charlie and sends Mikhail to The Looking Glass.He finds out that seven of the ten people he sent to the beach camp are dead. All that remain are Tom, Ryan, and Jason. They have Sayid, Bernard, and Jin captured. Bernard says that the rest of them went to the radio tower.
Ben allows Alex to go with him on his journey to intercept Jack's group before they reach the tower. Along the way, he communicates with Mikhail, telling him to kill not only Charlie, but Bonnie and Greta, too. He tells Alex that he is delivering her to her new family because she betrayed him.
When they meet up with Jack's group, Ben asks for five minutes with Jack alone. He tells Jack that Naomi is not who she says she is and Jack needs to give Ben her satellite phone or Bernard, Sayid, and Jin will die. Jack refuses to give him the phone and hears three gunshots over the walkie.
Jack beats Ben and forces him to go with them to the radio tower. At the tower, Ben begs Jack not to call Naomi's boat, but Jack does it anyway.
