How does the animator end the fight? By simply closing the document without saving.
Animator Vs. Animation 2
The Chosen One killing AIM by throwing the open AIM window at him, right before the Animator is about to be told how to defeat his creation.
The Animator defeating the Chosen One by using avast!.
Animator Vs. Animation 3
The Animator smacking the Chosen One aside in Microsoft Word with a over-sized "POW!"
The Dark Lord getting thrown into a Minesweeper game and tries to carefully tread his way out. The Chosen One blew the whole thing up by throwing Firefox into it.
The Animator trying to finish his game of Solitaire while the Dark Lord and Chosen One fight, not noticing them deciding to team up against him.
Earlier, he tries to continue the game while the Chosen One and Dark Lord are fighting within it. As they start blowing up his cards, he simply starts a new game right as The Chosen One is about to hit The Dark Lord with a card, causing the card to vanish and prompting The Dark Lord to just punch him. Then he drags them outside the game window—just dropping The Chosen One and carefully placing down The Dark Lord—like a parent telling his children to take their fight outside.
In a way, it's kind of funny how the Animator revives the Second Coming's closed friends: he refreshes the page, and there they all are, casually playing cards. It's also kind of funny how upon seeing this, the Second Coming immediately changes his mind about working with the Animator.
When faced with the prospect of leaving their window for the first time after The Second Coming broke in, all the fighting stick figures attempt to shove each other out as if they're saying "You first!" "No, you first!" until they all end up falling over. The Second Coming looks exasperated as he approaches the hole and just casually jumps out of it.
Animation Vs. Minecraft
When the stick figures are essentially playing Minecraft Creative Mode at the beginning, Blue tries growing plants with bonemeal, and ends up getting launched into the air by a rapidly growing jungle tree.