In Cotton’s boss lair, one of the sheep should be a less-than-corrupted Sixtyfour. If you rescue him during the boss battle, he thanks you with a useful item that isn’t too awesome to use, and scampers off.
This game is essentially derpibooru in a nightmare world. WAIT. TThe final boss, Spitfire (the derpibooru server) should look like herself, but hideously grotesque, an amalgam of all the users. Once you beat Spitfire She should dissolve revealing ClovertheClever, and then the universe around you dissolves, and then it’s just you, and Clover. Clover sadly explains that he broke the coding on Spitfire much worse than normal. She gained self awareness, and consumed all the users turning them into lifeless shells, and using them to create a prison for Clover. He then recreates her as her normal self, without the grotesque deformities, and explains how sorry he is to both of you. The void around you resolves into existence, and then everyone appears in Canterlot square. They all clap for you and shout CONGRATULATIONS! They all shout “SITE’S BACK UP!” And cheer.