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Gene's envy of Finny in A Separate Peace is what has caused him to jouse the limb of the tree, sending Finny crashing to the ground where he broke his leg. And, now that Finny is not around and is injured, Gene withdraws from athletics, choosing to be assistant to the crew manager, a position usually reserved for disabled students. But, when Quakenbush accuses Gene of being "maimed," Gene hits him violently across the face:
I didn't know why for an instant; it was almost as though I were maimed. Then the realization that there was someone who was flashed over me.
However, it is not so much that Gene defends Finny, but that he seeks to defend himself. For, at the end of Chapter 6, Gene Forrester remarks that when Finny telephoned him and said, "Listen pal, if I can't play sports, you're going to play them for me," he then again loses himself to Finny, feeling
a soaring sense of freedom [that] revealed this must have been my purpose from the first: to become a part of Phineas.
That Gene seeks to become Finny in his subconscious envy is certainly apparent. And, that because of this weakness of character he can find identity only by association with another person, Gene realizes he is, indeed, maimed and lashes out at Quakenbush for having perceived his flaws.
Gene attacks Quackenbush because he feels like Quackenbush is insulting Finny (since he's now disabled). Gene isn't maimed at all, which means cripple.d