The Unity was the name of the Master's vision for humanity and Pokémon alike following the events of the wars that created PMD-B. It required turning the surviving humans into Super Mutants due to the Master viewing humans as ill-suited to a world where Pokémon were the dominant beings, in order to bring world peace. It also involved using the Children of the Cathedral to find potential recruits and serve as a cover for his illicit activities while spreading his philosophy. The Lieutenant, the Master's second in command, also mentioned that once they were done conquering Angela, they would spread to Unova and gain control over the Entralink, allowing them to go on a war of conquest throughout the WAAPT Multiverse
Eventually the Unity ended due to the efforts of the Vault Dweller, Tracer's mons, and Team Taxonomy, and the survivors spread from Angela to other places in the chaos following their defeat.