A jobless person finds a job as a 'test subject' in Aperture Laboratories, and is asked to do a robotic surgery. After he wakes up, he is in Equestria. With no obvious way back, he asks a scientist to develop a portal, which requires a energy crystal. The energy crystal is in Discord's hands, and he has risen again.
[EDIT: This will be on hiatus for a while, because I'm too busy with homework and all those other stuff. If I remember this story, I'll continue.]