Due to pitifully low long-term conversion rates, the PER has decided that the best way to 'save' humans is to convert them against their wills. After several large potion bombings, the world drives them back into their homeland until the barrier is constructed as Celestia's last-ditch method of survival.
Unfortunately, this short war only brings about more supporters for the PER in Equestria, leading to the potion attacks on Gotham. These attacks were unprecedented in scale and in results. Hundreds of thousands of the residents of Gotham were forcibly converted, and, unfortunately, Bruce Wayne (Batman) was among them.
Besides from leaving criminals with much more freedom, this act of the PER also led to another unforeseen consequence: enraging the Joker. After all, he had finally found that which would finally break the spirit of both the city and the Batman, but it had all been ruined by the accursed ponies.
Now, with a thirst for bloodshed, he goes about repaying the PER for what they have done, his sights set on anything walking on four legs. However, as with many things the Joker is involved with, it may just fall into the disarray and chaos he is known for.
But who knows, the city may even consider him a hero after what he has planned for the equines...
EDIT: Rewriting this stuff. Will post next chapter when done.