Mario is walking to Princess Peach's Castle, when suddenly Kamek comes. He tells Mario that Bowser would love to have him as a bad guy, and then Kamek turns Mario into a Koopa Troopa. He meant to bring him straight to Bowser, but Mario manages to get away and since Kamek was in the air, he falls to a strange town called Koopasburg.
A Koopa named Koops and a Koopa named Kooper come up to Mario and both agree that he looks familiar. He explains why he looks familiar and then they tell him that they've turned evil. They're Bowser's Troops now. And they'll help Mario get to Bowser's Castle. Koops thinks that Mario should inform the main 7 Koopalings that he's coming to the Castle. Kooper thinks that the nearest Koopaling is at the Palm Portals.
At Palm Portals, Mario finds out that Larry Koopa runs the store. He is being attacked by Koopa Troopas and Handers. He begs Mario to go to the staff room to sound the alarm to get the Coppas out. Despite the big number of terrorists, Mario gets to the staff room, and sounds the alarm. The Coppas start attacking everyone except Larry. Mario defeats a few Coppas, and tells them that the other ones are the terrorists.
Larry thanks Mario and then he decides to test out a portal, and the portal leads to the terrorist fortress. Mario goes for revenge, and finds a lot of Shy Guys, and Yoshi Kids, to defeat. But Mario does it, and after hitting an EOL Block, finds that Yoshi is the terrorist leader! Yoshi doesn't notice that the Koopa is Mario, so he attacks!