In the final chapter of A Separate Peace, Gene admits to having killed Phineas as he reflects upon World War II:
I never killed anybody and I never developed an intense level of hatred for the enemy. Because my war ended before I ever put on a uniform; I was on active duty all my time at school; I killed my enemy there.
Further, Gene admits to having been involved in "an obsessive labor of defense...by developing a particular frame of mind" while he was in school against that whom he considered his "enemy...if he was indeed the enemy," Phineas.
In Chapter 4, when the envious Gene realizes that Finny really is a superior person--
Now I knew that there never was and never could have been any rivalry between us. I was not of the same quality as he--
he reflects, "I couldn't stand this." When Finny suggests that they have a meeting of the Super Suicide Society, Gene at first demurs, saying that he must study. But, then, because Finny has believed that Gene does not need to study, Gene does not want Finny to "excel me in this," so he agrees to go along. Thus, when they get to the tree and Finny suggests that he and Gene jump together off the limb, they climb up. Once there, Gene describes his action,
....Holding firmly to the trunk, I took a step toward him, and then my knees bent and I jounced the limb.
While Gene describes his action as not premeditated--inextricable--it appears to be a subconscious act of envy. It is this spontaneous act that Gene as an adult analyzes and concludes, as he does in the last chapter, was indeed meant to harm Finny.
As Ronald Weber writes in an article from Studies in Short Fiction, "It is Phineas's innocence that Gene cannot endure. As long as he can believe Phineas shares his enmity, he can find relief, but with this assurance gone, he stands condemned before himself and must strike out against his tormentor." (enotes)
At any rate, it is the first act of injurying Finny's leg that later leads to Finny's next injury in which, after he overhears "the trial" of Gene, plunges out of the doors and careens down the marble stairway, causingh his leg again to break. But this time, by a fluke, some of the marrow of his broken bone lodges in Finny's heart, stopping it. Indirectly, then, Gene is again responsible for Finny's injury, and, ultimately, for his death.
And he did everything he could think of for me. Ch.3