One of the biggest subplots is Stefan's trauma over the loss of his mother. During an early therapy session, we learn that Stefan had a favourite rabbit growing up. One morning, his dad took the rabbit while he was sleeping, and Stefan's desperate and prolonged search for the rabbit forces his mother to miss her usual morning commute train. The next train, which she catches, ends up crashing, leaving her dead. It's part of why Stefan is so messed up: he secretly blames himself for her death, and he resents his father for his hand in it as well.
Through a fun web of choices, you can opt to "retrieve" the rabbit from Stefan's father. This involves sneaking into his father's office and unlocking the safe. You have two password options: "TOY" or "PAC." With the latter choice, Stefan discovers that his father is not his father at all, but a scientist who is studying his experience with trauma. And his trauma is manufactured — they created the moment on a set when he was very young, as a way of "scarring" him. You can follow the conspiracy thread even more from there, or you can try the safe and use the other password.
If you input "TOY," all is normal and the trauma is real and the bunny is there. Through some strange time lapse, we're back at that moment, when Stefan loses his mother. Only this time, you have the option to board the train with her. Young Stefan dies on the train, causing present-day Stefan to instantly die in his therapist's chair. Which sequel to The Butterfly Effect is this, anyway?
I love this ending because it's incredibly hard to find, and it's probably the most "out there" choice you can land on. It renders the entire film useless, because Stefan never grows up in the first place. Time play has always fascinated me, and it's cool to see this take on it. A mind boggler for sure.