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In Season Three, the only way the Others had to leave the Island was the submarine. But if they used the submarine to leave the Island, they wouldn't be able to get back, as their underwater beacons showing the correct bearing to get to the Island without causing time-related problems as seen in "The Constant" had been knocked out by the Discharge from the Swan station in "Live Together, Die Alone."

As to why Ben didn't leave PRIOR to Season Three, he had only found out about his tumor just before Oceanic 815 crashed, so he needed to be able to stay on the island to monitor the situation. Also, given the Island's healing properties, he probably felt safer having the surgery done on the Island, where he would be less likely to die, and would have a quicker recovery time.

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