Gene attempts to be as honest as possible in his narration of the story. Despite his attempt to be completely forthcoming, there is one unanswered question at the heart of the story: Did Gene intentionally knock Finny from the tree?
Later, Gene's reasons for training for the Olympics, for visiting Lepellier, for hanging around Finny's sick bed are not clear to Gene as a retrospective narrator because they were not clear to Gene at the time these events took place.
Gene does not know the answer to this question of why he did certain things makes him an unreliable narrator, but only to a degree.
This specific lack of reliability directly relates to one of the novel's central themes, namely the theme of self-discovery.
On the whole, the story is not brought into doubt due to this question of intention in the tree. The facts of the story are clear and unaffected by the question of Gene's motivations.
The story gains an element of inquiry when we consider Gene's own inability to explain his motivations and even becomes a narrtive of self-exploration as Gene attempts, in telling the story, to come to an honest understanding of his motives and his feelings about the episodes in the story.
Also, as readers we can identify directly with Gene's uncertainly. His uncertainly is also our uncertainty as we read the novel, pressed with the same questions that Gene has posed to himself.
Built into the narrative style, with a story told as an extended flashback, there is an ambivalance that connects to and produces Gene's narrative unreliabilty as
...sometimes we are getting Gene's reaction at the moment and other times we are receiving the retrospective judgment of the mature man.
Ultimately, the effect of Gene's questionable motives is to suggest that the story is not about merely the facts of what happened in the summer and winter session. The story is about what the boys learned, about what Gene learned during this period and how he learned to decipher his own identity from those of his peers.