The canon ending of the books has Scott and Ramona deciding that even though they’ve both done bad things in the past, they both have earned a second chance with each other. They decided to go off and start anew, totally fresh, together. I should also note that in the books, NegaScott is absorbed by Scott prior to the fight with Gideon, and that’s what make him accept his past and decide to fight for himself and not just for Ramona. Now the deleted ending is in no way canon. Scott and Knives never get back together. However, given the difference in the books from the movie, this ending actually makes more sense for the movie versions of the characters. Scott and Ramona in the books actually do love each other, whereas they never share such close bonds in the movie. The books take place over the course of a year, the movie takes place in about a week. It’s believable that movie Scott would go back to movie Knives, since it’s shown they have a better bond. But it’s an alt ending because test audiences hated it.
I would highly recommend the books, any way you can get a hold of them. There’s a fuckton of awesome shit that isn’t in the movie, like basically most of the entire latter half of the books. it’s my favorite series for a reason. And that’s my half awake rant. It took me until right now to remember who you are because you changed your name.