Super Mario Minor Villains is an RPG for the Wii where several minor antagonists team up to rescue their bosses, closest friend, or something valuable to them. The gameplay is similar to Super Mario RPG, but there is different characters, Special Moves, Items, enemies and much more.
Baby Bowser is in his room, he got bored of playing with his things so he goes for a walk. When he returns, he finds a UFO above his castle and it beams it up into the craft, Baby Bowser is devastated with this and, with a look of determination, goes off to rescue it.
On Yo'ster Isle, Croco and his first, best and only friend Boshi, are about to have another race. The duo walk to the track and find a whole crowd at the stadium, The two of them take their positions and the announcer starts the race. 3....2...1..GO! Croco starts moving ahead but Boshi never started, then Croco see's a UFO floating over Boshi. It beams up and captures Boshi, Croco then sets out to rescue his friend.
Meanwhile, Doopliss is out helping his new friends, Beldam and Marilyn, find an ancient treasure, Doopliss is late and tries to make it before the other two leave without him, he is successful in making the trip but at that same moment, a UFO stops over the sisters and abducts them. Doopliss does not take this lightly and goes off to find the space craft.
In Goomba Village, Jr. Troopa is coming home from the Ice-Cream parlor and is about to go on his beloved playground, but when a UFO hovers over it and beams up his playground, he heads off to rescue his beloved playground.
On the Moon, Lord Crump is returning from a special mission and goes up into the main room, and is showing Grodus the magical gem that he had found on his journey. He is shocked to see that a UFO had just beamed up his master. Putting his hand on his heart, Lord Crump says "I will put every last effort of my strength to rescue you, master".
Afterwards, Midbus has just finished returning a giant wheelbarrow of Gold into Fawful's home and just enters the room when he finds a UFO beaming up his Lord. Midbus then sets off to rescue his Master, but is worried about him as well.
In another dimension, Nastasia is going to try to talk to Count Bleck. She got to the front door and thought about giving up, then Count Bleck opens the door. But after he opened the door, he got beamed up by a UFO. Nastasia then proceeds to rescue her crush.
After that, Popple is heading over to an ancient ruin when he finally finds the treasure that he has been searching for ever since he finished college. He is just inches away from getting it when a UFO beams it up. Popple is enraged and goes off to reclaim his gem.
All of the villains meet in the town square and they learn about each other's problems. Baby Bowser declares that they all team up and the adventure begins!