Here's a little bit of context for you guys in reference to Mewtwo and his Followers.
100 Years before the events of Pokemon Mystery Dungeon: Red Rescue Team and Pokemon Mystery Dungeon: Blue Rescue Team, the world was governed and protected by the Legendary Council. These were the Pokemon Arceus created to keep balance in the world he had created. Soon, more Pokemon were allowed to become Legendary Pokemon, becoming the Legendary Protectors.
One day, one of them commanded Arceus to become the new head of the Legendary Council. The Council was appalled at such a thing, and not only denied his request, but stripped him of his title of Legendary Pokemon. After that, he vanished.
Years later, he returned, demanding once more to be appointed the new head of the Legendary Council, but threatened war if his demand wasn't met. Once again, he was denied. If only they had known how prepared he was for the war he promised...
For years, the war raged between the forces of the Fallen Legendary and the Legendary Council. Eventually, it became apparent that the only way to end the war was to defeat the Fallen Legendary. One of the Legendary Pokemon, one whom once called the Fallen Legendary his brother, suggested a plan to bring the power of the Legendary Pokemon together.
It worked. The Fallen Legendary was defeated, the war ended, and peace was restored. However, there was a cost. The Legendary Pokemon were greately weakened, and could not protect the world as they once had. Soon, that duty fell to the normal Pokemon of the land, who created teams and guilds to help Pokemon in need.
Fast forward 125 years. The followers of the Fallen Legendary know it is nearly time for him to be revived. However, a prophecy was put into place that predicted not only that but that a new force of Legendary Pokemon would rise to stop him. His followers tried to prevent this, and almost succeeded. The Fallen Legendary was Revived, but as his numbers grew, so did the numbers of the Legendary Pokemon destined to stop him.
Once more, the former brother of the Fallen Legendary was called upon, and managed to defeat the Fallen Legendary and his forces. However, the Fallen Legendary managed to escape, while his most loyal followers were captured.
This story takes place ten years afterward. If you want to know more, I'm currently rewriting that story and will be posting it online soon!
(Also, if it wasn't clear enough, the Fallen Legendary is Mewtwo.)