Bowser tells him about Mario and Luigi ruining his plan and his chance of marrying Princess Peach. Tatanga tells him that he also has a plan and brought in his secret weapons,which turned out to be Wario and Waluigi.
Mario,Luigi,Toad,and Peach travels to Sarasaland to meet Princess Daisy,whom Luigi is smitten with. While enjoying the view of the desert,The Invaders attacks Sarasaland. Wario and Waluigi attacks Mario and Luigi while Tatanga kidnaps Peach and Daisy.
Mario and Luigi must journey to Chai Kingdom where Tatanga's goal is marry Daisy. They had to face 3 monsters from 3 Kingdoms. They are later confronted by Wario and Waluigi. They manage to defeat them and stops the wedding.
Mario fights with Bowser while Luigi helps Peach and Daisy fight off the enemy. Tatanga pilots his spacecraft and fires his Missles,releasing the molten lava. Mario attempts to save Bowser,but he refuses and allows himself to fall into the lava.
Mario and Luigi uses the Super Leaf to transform and defeats Tatanga by sending his ship into 100 feet in the air. Peach and Daisy congratulates Mario and Luigi,especially with Daisy kisses Luigi in the cheek. They went out on a double date.
Mid-Credits:
Toadsworth has heard the news of Bowser's demise and said "Good riddance". He was also informed that they found a secret file that was kept a long time ago,which make Toadsworth shock about Project Jr. Meanwhile in the lab,A capsule slips out. Inside of it is a little koopa that look like Bowser.
Post-Credits:
Wario and Waluigi survives the attack. Then,they notice the ripples in the lava. It began to bubble. Out of the lava was a Skeleton Claw.