The ending. Made even worse by everybody's shocked silence after they hear the words "GAME OVER. THE USER WINS.", only to have it broken by Dot's grief-stricken scream.
Surprisingly, Slash gets a minor moment when he laments the way things have been going in Mainframe lately.
"Bob always stopped us before we could do anything really bad. Now, nobody does."
The moment where Enzo, now Matrix, is reunited with Dot is a tear-jerker of a heartwarming sort.