The story goes that a Time Pony wants to grant other species the ability to regenerate. He envisions soldiers killed on the battlefield being able to rise up again to continue fighting. Murder victims being able to reveal who killed them. Deathly ill patients getting a second chance at life.
Despite all the potential benefits of sharing regeneration, the High Council protests and tells him not to pursue things any further. The danger is simply too great. The lesser races are just not ready for such power. They also state that the process of regeneration would be outright fatal to those not modified to handle it, meaning every species except the Time Ponies.
The furious Time Pony goes against the wishes of the council and manages to steal a vast amount of regeneration packets, which are what allow for a single regen each. He then steals a TARDIS and flees Gallopfrey, hoping to continue his work elsewhere.
The Doctor is assigned to stop him, resulting in a battle on the stolen TARDIS which causes it to eventually crash on a distant planet called Equus. Severe damage makes it very difficult to track down exactly where it went down. The Doctor returns to Gallopfrey to report what happened and seek advice from the High Council, and a way to find the scientist and stolen energy.
Meanwhile, the timeship’s descent is noticed by countless ponies and probably others. Unsure of what danger the unknown vessel presents to Equestria, Princess Celestia sends her faithful student Twilight Sparkle, to investigate the crash site. Worried for her safety, her friends accompany her on the trip.
Upon reaching the wreck, the Mane Six finds no signs of life in the ruins of the console room, but do find a strange container with something glowing inside it.
From the shadows staggers the renegade Time Pony, who proceeds to attack the Mane Six. Forced to defend herself, Twilight strikes the scientist down. Already badly injured, he promptly regenerates. The Royal Guards take him into custody and the container and wrecked TARDIS are confiscated and taken back to Ponyville, where Twilight begins studying the new technology in her laboratory.
Beyond this, I think what happens is the renegade Time Pony escapes custody and attacks Twilight to retrieve his property. The fight breaches the container and releases the regeneration packets all over either just Ponyville, the surrounding countryside, or all of Equestria.
The renegade is forced to flee, planning on finding and capturing those exposed to the energy. If he can take them back to Gallopfrey, it will prove that the process works and that he was right all along.
Back at the Golden Oaks Library, Twilight lies unconscious in the middle of her damaged laboratory. Badly injured by the renegade, she begins to glow with a soft golden light…
That’s all I’ve got so far. Ideas are always appreciated for a futur fanfic, if I ever get to writing it.