Team Protectorate: The Final Battle takes place in a supposed "End-Game" for the "Team Protectorate Storyline", during a time when specimens of every Legendary Pokémon species have been claimed by either Team Protectorate or Team Devastator, and Team Devastator is now on the warpath. Arming themselves and creating a massive airship meant to help them conquer the world, only one organization has the strength to stand in Team Devastator's way. Team Protectorate must gather its allies, and make a final stand against Team Devastator.