In the beginning of season three, Ben gives Juliet the task of interrogating Jack, while Kate and Sawyer are kept in cages. In the season 3 episode "Exposé", Ben and Juliet enter a Dharma station, the , and watch Jack on a monitor. Ben tells Juliet he will convince Jack to perform surgery on him. After Goodwin dies, Ben shows Juliet the corpse, so she knows she is Ben's and will be on the Island forever. He admits to Jack about having a tumor on his spine, and asks him to remove it in order for him to leave the Island. During the surgery he wakes up, where Jack refuses to finish until Kate and Sawyer are safely away from the Others. After they escape, Ben's operation is finished. He returns to the Barracks with the rest of the Others, and Jack in tow. When John Locke (Terry O'Quinn) comes to rescue Jack, he and Ben have a confrontation. Ben tells Locke of a "magic box" which can produce whatever someone wishes for and shows him his father, Anthony Cooper (Kevin Tighe), who they are holding captive and was brought to the Island because of the box. Ben offers Locke the opportunity to join the Others, but only if he kills Cooper; Ben knows he won't kill in cold blood, and so makes the offer as a way to humiliate Locke. Locke returns a few days later with Cooper's corpse, having used Sawyer to do the deed for him, so Ben takes him to meet Jacob. When Ben discovers Locke can hear Jacob, he shoots Locke and leaves him for dead. He returns to the Others' camp, and tells Richard, now his second-in-command, to lead the remaining Others to the Temple. Ben takes Alex with him as he attempts to prevent Jack from sending a radio message to a nearby freighter. He reunites Alex with her mother, and claims if Jack contacts the freighter, every single person on the Island will die. Ben is beaten and taken hostage, and forced to watch as the freighter is contacted.