Actually, there are three main crisis moments, which are also climaxes (heightened points of interest) on the story line.
In spite of their friendship and great complicity, Gene feels a twinge of jealousy when it comes to Phineas; upon a 'blind impulse,' he rocks the limb upon which Finny is perched (getting ready to dive), destabiles him and makes him fall from the tree. Finny, the great athlete, is crippled thereafter.
The next crisis happens just after the verdict of the kangaroo court: Gene is exposed for having deliberately shaken Phineas out of the tree; Phineas rushes blindly out, leaning on his crutches, stumbles and falls down the marble steps, breaking his leg again (and badly).
The final crisis is the conversation between Gene and Phineas at the hospital just before Phineas dies. Phineas, who has been in denial up to this point, confronts Gene about his betrayal, forgives him, but 'lets him go.' The rupture between the two friends is final, but it is the beginning of a self-awakening in Gene, who must come to terms with what he has done. (This is the resolution in process at the end of the novel.)
There is another subplot involving Leper and his tramautizing experiences in the war and subsequent breakdown, but on the main story line, the three moments of choice with no return (definition of a crisis) are as mentioned above. Note that within each one of these events there is a tandem cause-consequence effect, much like the piston motion Leper describes as a witnesses of the incident at the tree.