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Gene comments on how people "at some point found something in themselves pitted violently against something in the world around them." Finny didn't do this. Finny didn't pit himself against anyone. Finny created his own reality.
Gene says, "Phineas created an atmosphere in which I continued now to live," and he takes up Finny's way of looking at the world and choosing what to accept and what to let go. Because Finny is gone, Gene does have to let some of Finny's spirit reside in him.