This story is a sequel to Year Zero

Muffins at the End of the Universe IV

For many months Twilight Sparkle has pondered her role in the universe, while marooned in a crashed pod in the far future, eating reprocessed food and counting floor tiles to occupy her mind. Then she discovers a loophole in Equestrian colonial law, allowing her to rule over her new domain as princess, much to the annoyance of her colony's three citizens, Trixie, Derpy and Doctor Whooves.

As Twilight goes mad with power, treachery and revolution are in the air, as well as some explosive chemicals thanks to the Doctor, culminating in a finale of political intrigue involving a bubble wand and a rather dubious stick of celery.

This story is a sequel to The Enemy Within

Muffins at the End of the Universe III

Twilight Sparkle is facing the possibility that she may never return from a sunless, moonless, toxic wasteland, millions of years from civilisation. Still, that is no excuse to slip out of a good routine. Unfortunately, obstructions keep getting in the way, like supernatural encounters with fiery phoenixes, waiting in the dark.

It's Nightmare Night, and the scanner is clear (with the exception of a few muffin crumbs) for the first time in four months. Venturing outside, Doctor Whooves is delighted to find evidence of an alien intelligence, but everything is not quite as it seems.

This story is a sequel to Trixie Times Two

Muffins at the End of the Universe II

Being stranded in a crashed pod, millions of years away from civilisation, with no hope of ever getting back, is starting to have a negative effect on Twilight Sparkle's general well-being. Not helping are Trixie's attempts at mastering a teleportation spell, with varying degrees of success, or Doctor Whooves' latest crazy invention which goes wrong, with horrifying consequences, temporarily elevating Derpy to alicorn status.

But things are about to get a whole lot worse. Derpy is still unable to control her new powers (in spite of Trixie's perfectly faultless teaching) when a familiar enemy reawakens in the form of a giant muffin monster.

Muffins at the End of the Universe I

Trixie's attempt to perform a time spell leaves her and her mentor Princess Twilight Sparkle stranded two million and three hundred thousand years or something in the future. There they come across a pod occupied by Doctor Whooves and Derpy who have had a similar incident while testing a temporal drive (apparently it's quite common around this time of year).

Twilight has to come to terms with the fact that she may never see her friends again. Trixie, meanwhile, is tired of being under-appreciated and decides to use the Doctor's cloning technology to create the perfect companion. As if all of that isn't bad enough, the muffin supply is down to the last twenty crates.