A nuclear bomb goes of and Equestria spewing with radiation. Some of the ponies (including the main six) are able to survive and each create there own cults, and groups dedicated to there element. Some of the these thrive and become huge nations (such as rarity and and twilight) that stand out from the rest of decomposing and ruined land. In direct conflict with these nations are the fighting front(Apple jack and Rainbow dash) who want access to the these cites instead of scavenging and barely being alive. From inside the big cities, although the people know that there is a war, it does not affect them and don't really know what is going on. However, the soldiers can barely defend against the all out attacks of the rebels. Once they get inside they will behead the rulers (twilight and rarity) to and become better leaders that someday replenish Equestria to its former glory. Others are hidden away in the darkness (fluttershy) and have created dark cults driven by fear and sacrifice. These cults are not directly interfering with the war that is going on between the nations and the rebels. However, it is believed that in the future when the rebels take over they will be the the biggest threat that could end Equestria once and for all.
Skipping around 20 years in the future (the rebels take over and Twilight and rarity are killed off) science starts to become more developed, making this period turn into a steam punk age with developing science but only the older resources left from the bomb are left. Ponies begin to have enhancements to their body allowing them to become stronger and better. Also at this period ponies are just able to change between what they want to be, Earth, Unicorn or Pegasus. This becomes very controversial and the research ends up being discontinued. At this point the dark cult has had to elect three new leader since the demise of fluttershy, (radiation poisoning) Sweetie belle, Apple bloom and Scootaloo. They rename the cult the CMC. (the true CMC definition lost but they still remember those three letters). They begin to create hug battle machines that would seen in the steam punk age. This cult grows stronger and stronger until a point when it rivals the nations. The nations had known about this for a long time and decided to use there most powerful weapon at their disposal... an ion cannon. Although the CMC had not even attempted to harm the nations, they where obliterated from Equestria.
Skipping 800 years in the future, with Eqestria now grouped under under one nation, where space travel has allowed them to have different resources from other planets, has become a sort of Si-Fi place. Although they are not living with other aliens, they still have amazing technology that has caused them to increase life expectancy. One of the scientists working on dimensions was able to create a vacuum that instantly would suck you out to the corresponding alternate universe. The rulers Equestria decided to let there most powerful army leader with a select few citizens. Since they could not pass back though the vacuum, they were not told what they were doing. The group of 30 or so ponies were through out into a strange world that looked fairly similar to Equestria, but different and dark. The sky was full of floating grey ash that scatted the land. The plant life was long dead but it seemed as if the were living that way. There are some smears of blood that could be seen from time to time as they walked down the new land. Then from the shadows, an off yellow pony with a huge scar cut straight though eye appeared. Bloody hand prints are imprinted where her cutie mark should be. behind her some weak, powerless ponies are being dragged in chains, forced to be alive. Around 50 dark guards are awaiting at here disposal. She pointed to one of her slaves, a female child, and the soldiers dragged it in front of the group from the alternate reality. Using wide, rusty nails the soldiers stapled her hoofs into the ground. The child looked in pain but relieved and thankful that death would be upon her. the solder then cut down her chest so her organs where shown but he did not cut any vital parts of her body. It seemed as if the soldier was skilled at this. moments later unknown birds of prey flew down upon her. The first one dug its beak deep into her kidney and tried to pull it out. As the child screamed in pain, some chords where still attached to the kidney. With a snap of them, the child passed out and the other birds quickly moved in. At that point the child was dead. The woman who had ordered this slowly walked towards the carcass of the child and reach for a half eaten organ. It looked to be segment from her intestine but it was hard to know for sure since it was covered in blood. She then slowly devoured it, leaving blood smeared on her mouth. horrified by this violence, some of the citizens from the group of 30 passed out. Standing there confused, the army leader had just revived some intel from one of the historians in the group. They were taken to a reality where the evil cult had taken over! Then, at that moment they realized who that terrible woman was. It was fluttershy!