The central twist of "Good Will Hunting" is not a plot event, but a gradual psychological reveal of the depth of Will's trauma. Initially presented as a cocky, aggressive prodigy, the therapy sessions with Sean slowly peel back the layers of his defense mechanisms to reveal a terrified and deeply wounded young man. The key to this reveal is the discovery that Will was severely physically abused as a child by his foster father. He was given the choice of being beaten with a belt, a stick, or a wrench. This history explains his inability to trust, his fear of intimacy, and his violent outbursts.
The film's climax occurs in a therapy session where Sean, having seen photos of Will's scars, repeatedly tells him, "It's not your fault." This simple affirmation of his innocence as a child finally breaks through Will's defenses, leading to a complete emotional breakdown and the beginning of his true healing. Another significant turn is Will's decision to break up with Skylar after she asks him to move to California with her. He pushes her away out of fear, lying to her about not loving her to avoid the possibility of her one day leaving him.
The ending sees Will rejecting the prestigious job offers that Professor Lambeau has arranged for him. Instead, he leaves a note for Sean, echoing Sean's own life-changing words: "I had to go see about a girl." He then drives off in the car his friends bought him, heading to California to reunite with Skylar. This ending signifies that Will has finally chosen to pursue emotional connection and love over intellectual pursuits and the expectations of others, fully embracing the lessons he learned from Sean and taking control of his own life.