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Don't confuse this with Super Mario RPG, an actual Mario game for the SNES.
Bowser has kidnapped the princess again. It is up to the Mario Bros. to save her, like always. When the Mario Bros are escaping Peach's castle, they encounter a Goomba. Like in the Mario & Luigi RPG games, Toadsworth teaches them how to battle. Shortly after, the Mario Bros. learn that Goomboss has been capturing a lot of Toads. Mario and Luigi get to Goomba Castle and defeat Goomboss. All of the Toads are freed,and one joins the Mario Brothers.
Along their journey, they find a pipe. They end up back at Peach's castle. Bowser's airships were launching a sneak attack on the Mushroom Kingdom. Mario, Luigi, and Toad manage to get on the airships, because one of their anchors was down. The airships fly away. Mario and co. decide to find who was leading the attack. They get to the largest airship, and they find Bowser Jr. Mario, Luigi,and Toad manage to defeat Bowser Jr. The airship they are on ends up crashing into the sea. Bowser Jr. runs off, trying to find a way to find land.
Mario and co. encounter a giant Blooper. The Blooper attacks them,and the Mario Bros. and Toad defeat the Blooper. When Mario and co. are almost at land, they see a Sushi. Sushi tries to eat Mario and friends, but they defeat it. When they finally make it to land, they find a jungle. After they explore through it, they find a treehouse. Mario, Luigi, and Toad are relieved to see that there is life on the islands other than enemies.
When they go to see who is in the treehouse, Donkey Kong comes out. Mario and friends ended up at Kong Island. Mario and friends tell DK what happened, Donkey Kong decides to help Mario and co. escape Kong Isle. Donkey Kong tells Diddy Kong what happened, they join Mario's party. After exploring through Kong Island, Mario,Luigi,Toad,DK, and Diddy encounter King K. Rool, who's pirate ship is bombing the island with cannonballs. Mario and co. defeat King K. Rool, and they see Enguarde in the ocean. DK tells Enguarde what happened. Enguarde agrees to help Mario, Luigi, and Toad.
He takes them to the nearest land, and they find another island. At that island, they see Yoshi. Yoshi decides to help Mario,Luigi, and Toad rescue Peach. Yoshi says that they must climb up to the highest point on the island, and a giant Goonie will give them a ride. They get to the top, but Yoob is there. Mario,Luigi,Yoshi, and Toad defeat Yoob. A goonie comes and takes them back to the mushroom kingdom. Mario and co. go into a cave. They find Morton Koopa Jr.,Roy Koopa,and Larry trying to steal gold from someone. It is a Toad which was mining for gold in the cave. Mario and co. decide to help and defeat Larry,Roy,and Morton. The gold miner Toad decides to join Mario and friends. After going through the cave,they find Petey Pirahna. He tries to eat Mario and co. but they defeat him. Later, they find a mansion. Boos come and capture Mario and friends, but Luigi avoids them.
Luigi goes inside to rescue Mario and co. When he finds the secret room, he sees King Boo, who captured everybody. Luigi defeats King Boo and rescues his brother and his friends. Later, they see a mountain. When Mario and friends climb up it they find the cloud world. But then, Bowser Jr.'s airships come. Mario, Luigi,etc. jump on to the ship and hide in barrels.When the ships land at Bowser's castle, Iggy,Lemmy,Ludwig,and Wendy O. Koopa sees them. Mario and co. defeat the Koopalings and go in Bowser's castle. Mario and co. encounter Bowser and Bowser Jr. Mario and friends defeat them.
DK (Kong Isle only)
Diddy Kong (Kong Isle only)