TEAM LEADER: The Shredder / Oroku Saki
1st Draft: Darth Vader
2nd Draft: Apocolypse
3rd Draft: The Joker
The Shredder has led the Foot Clan and is one of the greatest ninjas to ever live and a born warlord. If a world threat were to happen he would not allow for any other person to rule above him.
Darth Vader has been second in command to the Galactic Empire and is the strongest known entity in the Force, able to bring down and crush Star Destroyers with his mind alone.
Apocalypse is the first and arguably the strongest mutant on earth, able to grow in size by 1000% and transform his limbs into powerful weapons at will.
The Joker is the wild card chaotic and destructive with a flare for the theatrics. He doesn't think like a regular person so he is able to see flaws he can exploit that nobody else could. Of all in the team he is potentially be the most dangerous.
Though they are all villains, they're combined abilities could easily save the world from any threat that did not fit into their own machinations. That is if they could work together long enough.