Three significant instances of inner conflict affecting Gene's decisions and subsequent behavior are these:
- inner conflict over the idea that Finny is trying to sabotage Gene's studies.
- inner conflict over feelings of inadequacy when compared to Phineas, whose charm saves him from repercussions of his (mis-) behavior
- inner conflict of guilt over the consequences his irrational act caused in Phineas's life
The first two instances are critical to the major story conflict, to the climax and to the resolution. Since Gene suspected Phineas (Finny) of trying to interfere with his studies--thus making him fail to some degree or another--he feels the weight of his feelings of inferiority and inadequacy when Finny unknowingly proves to Gene's satisfaction that sabotage is neither his thought nor intent. It is these feelings, following in the wake of disparaging thoughts about Finny, that make Gene decide to go to the tree after all, (2) to agree to a double jump with Finny and (3) to act out impulsively from internal agitation to antagonize Finny.
The third instance leads Gene to decide to tell Finny that the accident was the direct result of Gene's choice to jounce the limb so Finny would fall, thereby confessing his guilt for Finny's condition as an invalid. This confession adds to the emotional agitation Gene feels about Finny and about the war through the rest of the story. It also compels his decision not to enlist for the war effort like Leper did.
[Gene said,] "I was thinking about you ... and the accident."
[Finny said,] "There's loyalty for you. To think about me when you were on a vacation."
"I was thinking about it, about you because—I was thinking about you and the accident because I caused it."
Finny looked steadily at me, his face very handsome and expressionless. "What do you mean, you caused it," his voice was as steady as his eyes.
My own voice sounded quiet and foreign "I jounced the limb. I caused it." One more sentence. "I deliberately jounced the limb so you would fall off."
He looked older than I had ever seen him "Of course you didn't."
"Yes I did. I did!"
A very important fourth instance of inner conflict driving Gene's decision is his underlying fear of being inadequate to the demands of life, a feeling accentuated in the shadow of Finny's seemingly god-like powers, charm and successes. Gene ends his narrative by revealing that his fear was common to and shared by all the boys he knew at school.