On the note of it being something like pokerus, it could be like the Rage Virus like in 28 Days/Weeks Later. Not only do Pokemon reach their max potential faster and easier, but the pain they feel is dampened or completely absent. The new strand of pokerus might make them extremely hostile, making the pokemon like a perfect fighting machine that doesn't hold back and doesn't give up. This would sound perfect for either an underground to-the-death pokemon fighting organization, with secret broadcasts and bets and such, or an agency interested in fighting with pokemon for control again (like how the two kingdoms fought in the Lucario movie).
Or we could get even more similar to 28D/WL and have it be a strand of pokerus that scientists were trying to tamper with, but turns out to unlock the ancient potential of the illness that was tampered and bred exactly for full-out war, except maybe worse. This strand may become advanced and turns into the 'self-aware' kind of virus, wanting victims for food and to spread the disease (but usually not both at the same time).
Welcome to the world of better, faster, stronger and super-powered pokemon 'zombies'.
(as a note: the fact of whether the pokemon are still alive or reanimated is still completely up in the air, I just took some movie inspiration and ran with it)
(another note: anyone else liking the idea of a pokemon world ravaged by war and THEN being inflicted with zombies? I think the end of the war would be quite an interesting starting point for an RP like this, people relieved and letting their guard down while their pokemon get restless.)
