(ALTERNATE ENDING) Rocket to insanity: dawn of a dying Pegasus: the broken allegiance

The Doctor trotted cautiously toward Sugarcube Corner. He had crash-landed on this planet in an abandoned warehouse in his TARDIS around a year ago, picked himself up, discovered he had become an equine, et cetera, and had set off toward the nearest town, Ponyville.

Back in the present. His timey-wimey detector had gone ding, indicating there was stuff. (Yes, I went there) in this case, a series of violent events would occur soon, the first of which, was at Sugarcube corner. As he looked in the window, he was just in time to see a conversation between a cyan Pegasus and a pink party pony.

“No...no...nonononononoNONONONO!” Rainbow yelled, her eyes darting around. “N-no...no, I don't want 'em. Not gonna l-let you...lemme out of here, LET ME OUT OF HERE!” She then proceeded to stab Pinkie, babbling something about how she should've stayed away. When she saw what she had done, she started sobbing uncontrollably. However that sobbing soon turned into hysterical laughter, and then she left, leaving the Doctor alone with Pinkie's corpse. As he entered Sugarcube Corner, an idea struck him.

"Is it..." He wondered. "Can I...yes, I think I can!" He then teleported Pinkie's body back to the TARDIS, in the freezer to be preserved, stealing it from the morgue shortly before the autopsy was due.

"I'll have to get the other bodies too," he thought. "Next is Applejack." He then hurried to Sweet Apple Acres.

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He arrived just in time to see Applejack thrown onto the pitchfork.

"W-huh. .... W-why?" Applejack choked, coughing up blood with each syllable. The pegasus didn't answer, she just started to sing as she advanced with the splinter in her hoof. She used her wings to match her friend's height, using her free hoof to hold Applejack by the neck. The Pegasus just stared at Applejack, watching her fear build, as she brought the wooden blade back for the fatal blow.

After she left, the doctor took the body like with Pinkie, and proceeded to follow Twilight Sparkle. She would probably want to find and cure Rainbow; after all, they ARE the elements of harmony.

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Eventually Twilight came to a library in a different town, proceeding inside. Likewise, the Doctor watched them talk to a unicorn through a window, barely able to catch parts of the conversation, though he did hear the unicorn say something about Rainbow Dash possibly being poisoned with an extremely powerful hallucinogen.

"Aha! That must be why she's going around on a killing spree!" The Doctor thought. "If I can cure the poison with THAT power, I could stop her insanity!"

He then sped toward the next site of death.

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After taking the bodies of the fallen 5 (he killed the timber wolves and teleported the rest of the bodies before anypony could see) he hurried back to Twilight's library, setting a scroll on her doormat containing an important message. Now all he could do was wait, and hope she did the right thing...