Mushroom Plains - Bowser and his army start attacking the castle and kidnap Princess Peach.
Undergrounds - Mario and his team head into the undergrounds as a quick passage to Bowser's Castle but discover from Petey Piranha that they have not taken Peach to Bowser's Castle.
Yoshi's Island - to get more intell the team heads to Yoshi's Island where Kamek has taken brainwashed all the Yoshi's, including the original one. However after beating Kamek they find out Bowser's true location.
Palace of Shadows - Mario and co. first have to break through the defenses of Bowser Jr., Kamek and Basilisx. As they proceed to Bowser they discover that Bowser has been taken over by Shadow Queen. She leaves Bowser's body and enters Peach's. She then uses magic on Mario to split him into four different versions of him: Metal Mario, Cosmic Mario, Shadow Bug Mario and Shadow Mario, with the latter entering Bowser Jr's body and flees the place. The other three get send away while the regular Mario is in a comatose state transported somewhere out in the desert.
Bob-Omb Battlefield - Captain Toad and Luigi travel to the Bob-Omb Battlefield where they see that Metal Mario has taken over Bob-Omb King. They defeat Bob-Omb King but Metal Mario flees.
World Bowser - The duo continues and find themselves in World Bowser where Metal Mario indeed is. They defeat him and restore a piece of Mario's heart. Hisstocrat has to be defeated in order to get to the second part of the map.
Bianco Hills - Daisy heads to Bianco Hills where she meets with a little Noki girl who she wants to protect. She must defeat Bowser Jr. while also fending off Petey Piranha. After Shadow Mario is driven out of Bowser Jr. he sides with Daisy with the reason that this isn't something his dad would ever do.
Delfino Plaza - Upon arriving in Delfino Plaza they need to defeat Shadow Mario, but are faced by Gooper Blooper who gets in their way.
Good Egg Galaxy - Yoshi heads to the Good Egg Galaxy and searches for Rosalina who apparently got controlled by the Cosmic Mario turning her into Cosmic Rosalina. Upon defeating her the Cosmic Mario flees but Dino Piranha shows up to kill Yoshi and Rosalina.
Honeyhive Galaxy - The Cosmic Mario locked up Honey Queen and made her bees its own. Rosalina and Yoshi have to free Honey Queen so the bees join their side and then they must defeat Cosmic Mario who then will be send to Mario again.
Shadow Bug Mario
Forest Maze - Prince Peasley heads to the Forest maze where the Shadow Bug Mario has awaken Geno again. Peasley must fight him in every keep that he turns to, until reaching a dead end at the Tadpole Pound. The Shadow Bug decides to leave Geno's body who the remains active. Geno says he will aid him to save Mario.
Nimbus Land - They head to Nimbus Land where Belome is attacking Mallow's castle. Only after defeating Belome the Shadow Bug reveals itself. The trio defeat it and it returns to Mario's body.
Gritzy Desert - Everyone returns safely and try to track Mario's body which is held captive by Nabbit to sell for money. Luigi, Cp. Toad, Daisy, Yoshi and Peasley try to defeat him although Wario and Waluigi aid Nabbit as they adore money. After getting Mario's body back Nabbit apologizes wheras Wario and Waluigi have fled. Mario however doesn't seem to revive. They call E. Gadd who tells them his heart needs a push to work again. He tells Luigi that there is a device in Evershade Valley that can do the trick.
Evershade Valley - The gang arrives at Evershade Valley. They have to eliminate all the Bogmire's in order to make King Boo appear, and need a key to enter his keep. Once they have done that they defeat King Boo, retrieve the device, and head back. They revive Mario and can go on again.
Frozen Peeks - Bowser wakes up next to Fawful and the two, although not liking each other, decide to team up to get out of this place. They encounter Chakron who they have to fight to get information out of him. Chakron only can be fought upon retrieving the key belonging to his keep.
Bowser's Castle - Bowser and Fawful head to Bowser's Castle where they are stopped by Boomer who now keeps guard of it, being brainwashed by Shadow Queen. They defeat him and bring him to his senses. The three enter the castle and have to clear all the keeps and free the prisoners: Kamek, Petey Piranha and Basilisx.
Castle Bleck - After Bowser learns that Shadow Queen is behind it he requests to go and visit Count Bleck with whom he still is on bad terms with. He along with Fawful, Kamek, Petey and Basilisx head there. Fawful however turns traitorous, so Bowser, Kamek and Basilisx have to defeat both of them. In the end Count Bleck says there is a way to defeat the Shadow Queen with ease.
Palace of Shadows - Mario and co. head to the Palace of Shadows to confront Shadow Queen. She keeps herself secured in the final keep. They have to make her way up there however Dark versions of the heroes have appeared on the map. Eventually Hooktail also shows up. Before the time runs out you have to defeat Shadow Queen and turn Peach back to normal. Shadow Queen flees soon after.
Star Hill - both teams now head to Star Hill to confront Shadow Queen. Although only the hero team is playable, and side characters assist, while the villain team (Bowser Jr. joined that team now of course) is also there to be beaten. After beating the Shadow Queen, Bowser interrupts and inhales her essence leaving Bowser with a purple essence surrounding him. The creature leaves soon after.
Mushroom Plains - Bowser wrecks the whole environment and Mario has to defeat him. However after defeating him he turns into Giga Bowser because of Shadow Queen's essence. After Giga Bowser is killed all is good again.