This story is a sequel to Upheaval: Breaking Point

Following the events of Breaking Point, Twilight Sparkle and her friends discover that Equestria's demise may not come from an enemy invasion, but from within. The Barrier Lands and the Heartland begin the slow and uneasy process of reuniting into a single Equestria, but this long-delayed joining is already in danger at its conception.

With Celestia's power in her grasp and her agents by her side, the wheels of Black Rose's plans for Equestria's future continue to turn. However, her brazen gamble has done more than just bring down a centuries-old barrier. Ancient powers begin to stir: the remnants of a dark period in Equestria's history, the immortal inhabitants of Celestia's homeworld, and a rising tide of darkness coming ever closer.

FAQ for this story: FiM Fic version and GDoc version (constantly updated and edited)

The Wandering Physicist is a mysterious traveller who just arrived in Ponyville. After establishing himself in the video game shop, he begins his encounters with the denizens of Ponyville. This sets off many ongoing adventures with his new friends. With a constant stream of visitors from around Equestria, friendship, family, twists and turns and legions of nerds are on the horizon.

Setting: Approximately a year after the end of the series.

Character References: On tumblr - On Deviant Art - Warning: Contains spoilers and peanut products.

To new readers: These were written as an ongoing serial. The individual story does not necessarily carry chapter to chapter, but the continuing story and events carry over. Feel free to skip around the chapters without losing too much continuity. If you do not wish to start at the beginning, Crossroads is a good starting location as it lays down the groundwork most of what follow.

As this was a serial, there is a cast list at the top of each chapter allowing the you to read only those with characters you are interested in. The main characters listed are those that appear in the majority of the chapters.

Arcs:
TWP vs the World: The Game Arc - A Trixie Situation to Final Boss - Trixie is on the run from some nasty elements in her family. Ponyville is placed in gaming illusions to force TWP to turn Trixie over.
The Physicist's Wife Arc - The Physicist's Wife to Confessions - Fluttershy gets injured and thinks she is married to The Wandering Physicist. She spends a month living with her love, but what do her friends think of the new Mrs Wanderer?
Adventures in Neighpon - Turning Neighponese to Tomodachi Sketch - The Wandering Physicists takes his friends on a trip to Neighpon. A series of interconnected adventures take place leading to love, fortune, action and a giant alicorn plushie.

Prequel to The Master Game
Prequel to Starlight Chronicles

A horrible Cataclysm has turned all of Equestria into a Wasteland of barren ash and twilight desolation. The Sun and the Moon have been destroyed. Everypony has died--including Princesses Luna and Celestia. But one pony miraculously survives; she is a lone wanderer, the last of her kind, surrounded by menacing creatures that hate her. She navigates the Wastes in an airship and scavenges off the blighted landscape to keep herself alive.

Then one day she meets an old companion who grants her a gift, the chance to go back in time to the warm and sunny days of Ponyville, where her dead friends live in happiness. How far will the last pony venture into this joyous age of Equestria, even if she fully knows that there is no way to change the horrible fate of everypony she loves?

2013 Edition: Smaller Chapters, Better Grammar, and a Few New Scenes

(A shout-out to Vimbert, pre-reader and gentlecolt)

This is a fic based on the Time Loop Files, the format of which was first codified by Innortal on fanfiction.net.
Here's a brief guide.
The basic idea is, one character (the Anchor, usually the main character of a fictional setting) is looping back to the very first moments of their parent series every time either they die or some kind of time limit expires. They of course end up monumentally stir crazy given enough time.
Eventually others start to loop as well.
The reset is not always perfect. Sometimes a loop's history will be different to the "prime" loop, or canonical plot.
"Crossover" or "Fusion" loops also occur, randomly. These can involve the home loopers having a guest, or the anchor for one universe spending time in another, or replacements of one character by another.
Vacation Loops are where the Anchor (or others) decide/s "buck it" and lets off steam by doing whatever comes to mind. There's little or no attempt to maintain the original timeline.

In addition, and particularly more recently, it should be known that this story has a collaborative element to it - people may submit loop ideas or loops, ideally at the Spacebattles thread (a link to the current version of which is on the Trope page), and they may become included.

There's two page image options, thanks to Filraen - the current page image has been edited by the original creator from this work of theirs.. The other one is here:
http://hourglass-vectors.deviantart.com/art/MLP-Loops-466030169