"I have sworn upon the altar of God, eternal hostility against every form of tyranny over the mind of man." —Thomas Jefferson
Three-hundred years after Equestria failed to overtake the human race, humanity took to the stars. The newfoals left behind by Celestia's hasty retreat, as well as the ponies trapped on Earth after the war, have integrated into humanity, with both races eventually regarding each other as equals.But now, in a distant corner of the universe, a colonization ship known as the Calvin has discovered a small bubble of warping space-time on an otherwise uninhabitable planet. It's exactly the same size as the one that appeared on Earth many years ago. Wouldn't you know it, it was exactly what had appeared the planet all that time ago.The Conversion Bureau: Conquer the Stars is an in-progress fanfiction by Dalek IX, the same author of A Hero and Friends of a Solar Empire. As of right now, it's available to be read on the Space Battles forums right here (with chopped up scenes, and discussions) and here (a story only thread). There is also a copy on FIMfiction, here.
Breaking the Fellowship: The Mane Six is officially disbanded, as Fluttershy burned all bridges with them and went into hiding with her animal buddies. Reactions to this event were mixed: Dash feels extremely hurt by it, to the point where she regularly flies over the Everfree in search for her; Twilight insists in believing the Princesses were right (though mostly because she's in denial and doesn't want to believe her mentor could ever be wrong about anything); Rarity is trying to pretend nothing's wrong; Applejack, due the shift leaving both Appleloosa and a large chunk of the Apple Family behind to fend for themselves, is starting to doubt Celestia as well; and finally, Pinkie's desperately trying to hold her remaining friends together.
Bully Hunter: Firebird got her cutie mark (a pair of swords crossed over a shield) defending someone from a gang of bullies.
Chekhov's Gun: In Not Alone, the last scene is Celestia reading a letter from Queen Molyneux of the Gryphons, telling Celestia that her Omniscient Morality Licence has been revoked. The backstory of this fic shows that this led to the Gryphons, Zebras and other species in their world to wage such a devastating all-out war with Equestria, it forced Celestia to "jump" their land again, only this time, a good deal of it was left behind.
Crapsack World: Equestria. Economic collapse and war has decimated the country, and forced Celestia to jump onto a planet that is just barely habitable. Meanwhile, the Calvin suffers from overpopulation, lack of resources and crime. Even so, both have places where the crapsacky-ness is especially pronounced: Equestria has Hoofington, and the Calvin has Sector 12.
Death World: The planet Equestria relocated itself to. Not only is it a barely habitable freezing ball of ice, but (as Twilight notes) it's also infested with dangerous beasts that would make anything from the Everfree Forest look downright cute and cuddly in comparison.
Even Evil Has Standards : Apparently, the Changelings fought alongside the other races against Equestria during the war. Although whether it's this trope or if they're simply looking out for their own interests at heart remains to be seen.
Freudian Excuse: Firebird's parents are Newfoals, which made them total doormats who were unable to deal with their daughter's fiery personality. They also couldn't come to terms with her cutie mark and even more, Firebird seems to strongly feel she should've been born a human but was cheated out of it.
Humiliation Conga: After the Gryphon Queen declared Celestia's Omniscient Morality License was revoked at the end of Not Alone, Equestria goes through this. First, all of the other countries in Equis launch a massive economic embargo on Equestria, forcing the heavily import-dependent country to develop on its own, while dealing with scarcities of several different resources in the meantime. Some time later, negotiations were re-established for the next five years, during which things seemed like they'd be okay... only for, on the fifth Hearth's Warming Eve, all nations to declare war on Equestria simultaneously. The following campaign was so devastating to Equestrianote even Celestia herself plus an entire armada of her best royal guards were crushed by Gryphon's fleet in front of the entire populace of Manehattan that the Princesses were forced to relocate to another planet (see Death World above), and even that was done by leaving several pieces of Equestria, like the entirety of Appleloosa and literally half of Hoofington, behind. By the time the USS Calvin discovers Equestria, the country is ravaged by civil war, extremely impoverished, has lost use of the Elements of Harmony, and a resistance movement is midway through a plan to "bring the Princess to her miserable knees".
Despite being uninhabited, Hyperspace is very freaky on several levels. To the naked eye, it's a black void completely devoid of light. Radar gives constant false readings of things that accelerate way to fast and occasionally pass through the ships. Thaumic sensors go completely berserk. LIDAR... forget about LIDAR. It's also full of hydrogen, which ships can harvest as fuel using Bussard Scoops.
There's enough hydrogen to transmit a Sound that exists in frquencies beyond normal hearing. The only time that someone managed to translate The Sound of Hyperspace into something audible, all those who heard it committed suicide and several more were murdered by the one person who didn't. It's standard protocol for ships to have no contact with anything outside the ship during transit.
La Résistance: This is building up in Hoofington for the reasons as illustrated below. A small group of gryphons, zebras, changelings, minotaurs, and elk that got carried over in the severing are also in the picture.
Equestria as a whole. After the mess on Earth and the other species (the gryphons, zebras, minotaurs, elk, and buffalo) catch wind of what the princesses tried to do, they cut off all ties with Equestria, causing economic collapse. And then they declare war, in which Equestria loses ALL of their coastal cities, along with Manehattan, Appleloosa, New Pegas, and half of Hoofington, forcing them to dimension jump to another world. And that's not to mention that a good number of ponies are siding with Equis' other species who were pulled during the "jump" and the more war-torn areas like Hoofington are on the verge of openly revolting against Celestia and Luna.
Twilight herself is on the receiving end. While her friends don't blame her for anything that's happened, both she and the rest of the ponies do, having marked her and ostracized her as a social pariah to the point she seldom leaves the library these days.
The Matchmaker: Firebird, of all people, tries to hook up Evening Star with Steel Prism, a cop and her escort during the undercover mission to Equestria.
Medieval Stasis: It's been several centuries since Not Alone. In that time Equestria hasn't really developed much technologically and apparently the events from Not Alone only happened recently for them (though this can be justified by the fact that Equestria's economy has gone down the drain and time likely passes very differently for them). Meanwhile humanity and the ponies left behind have not only achieved peaceful coexistence, but have also conquered the stars together.
Multiple-Choice Past: Firebird. Evening notes that every time she asks her about what her life was before becoming a thug, she spins a different story.
Social Services Does Not Exist: Justified with Firebird, and presumably others like her. Due to escalated crime rates, lack of resources and overpopulation resulting in seedy slums, several people just fall through the cracks. Luckily, Firebird does get help later on.
Sophisticated as Hell: Sunny Disposition manages to combine extremely technical language with copious amounts of swearing.
Tranquil Fury: When Firebird gets really, really angry she becomes "as cold and as emotionless as the void of space".
We Are as Mayflies: The ponies can naturally live for a good few centuries, which was a problem for Evening Star, one of the ponies present in Not Alone and who obviously outlived her human friends. It's averted later: through the applications of both new technology and magic, humans can live just as long as their four-legged brethren, sometimes even longer.
We Could Have Avoided All This: It's for this exact reason many of Equestria's residents have lost a lot of love for the princesses, due to their actions on Earth leading to economic collapse, war with the other species, and being forced to "jump" dimensions, and are teetering on the edge of a full blown rebellion. Twilight also feels this way in regards to her disastrous interview.