When Humanity met Ponykind, things went poorly for Humanity. Ponykind eventually won, but a Unicorn named Prancer blames humanity for every death in the process, and especially for the problems Equestria ran into when the war was over. Surely, humanity's evil nature must have rubbed off on Ponykind! That's the only explanation she's willing to accept. Determined to set things right, she travels back in time, and sets out to solve the problem by turning herself into a magical virus designed to "Take the evil out of Humanity", while making them stronger, smarter, and more magically powerful in the process.
What could possibly go wrong?
Disclaimer: The story's protagonist hates humanity, I do not. If you hate Prancer, or think she's an arrogant prat, it's because you're kind of supposed to. She blames humanity for Equestria's desire to from-a-certain-point-of-view semi-genocide humanity, man, and she decides the best way to fix the solution is to magically "Fix" humanity before Equestria sees it. I don't agree with her views, philosophy, or methodology. Or her quickness to assume that if Ponykind does something she doesn't like, humanity must be to blame. This is a work of fiction, any resemblance to any characters, people, or worlds, living or dead, is entirely coincidental.
Remember, TCB isn't anti-humanity, it's anti-TCB humanity. That particular future version of humanity that destroyed its own planet and has no future. In this setting, choosing to remain a human and die a human would make about as much sense as a human refusing The Doctor's aid, refusing to get into the TARDIS, and choosing to stay on earth and "Die a human" by dying when the earth is swallowed by the sun. Same goes for trying to stop The Doctor, or in this case, Ponykind.
