why does the exposure of lepers deranged hallucinations bring the two boys close together?

They see what the war has done to him and realize that there really is a war going on.

Gene has just visited Leper after he has gone A-Wall (run away from the military). Leper rambles on about his many mental problems finding time to also accuse Gene of hurting Finny. What Gene takes away from this is that all the boys are essentially fighting themselves. They don't know who they are inside and end up in conflict with each other to find out. Gene and Finny had identified themselves through this conflict. Gene realizes that he needs to distance himself from Finny's conflicts and find his own "separate peace". Ironically this realization helps Gene deal with Finny more constructively and brings them closer together.