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Mario, Luigi, Princess Toadstool and Toad have travelled to Down Under Land, where they are searching for a Magic Statue that can supposedly protect Princess Toadstool's kingdom. Walking past several Birdoroos, the quartet approaches a small town.
In the town, King Koopa sneaks over to the Magic Statue, picks it up, and runs off with it. As King Koopa runs past City Hall, the mayor of the town refers to him as Kangaroo Koopa, and pleads for Mario's group to stop him. Before they can react, Kangaroo Koopa runs past them, claiming that the Magic Statue is now his, and that the crocodiles that suddenly start infesting the town are theirs.
With Kangaroo Koopa gone, the mayor explains that the Magic Statue was his town's only protection against the crocodiles, who will inevitably eat everyone there if they're not stopped soon. While Mario laments about not being able to eat lunch, a crocodile creeps up behind Toad. Mario states that if he doesn't get to eat anything, neither should the crocodile. Mario attempts to wrestle the crocodile, but soon gets himself knocked off its back. Luigi fearfully attempts to fend off the crocodile with his plumber's helper, but Mario pulls out his own and uses it to keep the crocodile's mouth wedged open.
Princess Toadstool congratulates Crocodile Mario, but she and Toad are then chased off by another crocodile. The mayor directs the two of them to hide out on top of the general store with the rest of the townsfolk, where the crocodiles can't reach them. As all the buildings in town are made of wood, the crocodiles start chewing the walls of the store in an attempt to bring it down. Princess Toadstool begs for Mario and Luigi to retrieve the Magic Statue. Mario complies, but he and Luigi are surrounded by the crocodiles, one of which spits Mario's plumber's helper back at him.
With nowhere to run, Luigi states that the crocodile Mario that stopped earlier has recuited his friends to help him finish the two of them off. Mario tells Luigi to piggyback himself onto his shoulders, and using his plumber's helper as a pogostick, they bounce over the crocodiles and escape from the town. Though Luigi comments that the two of them are now safe, Mario states that Princess Toadstool and Toad are still in danger, and that they still need to get the Magic Statue back from Kangaroo Koopa.
After constructing a raft, Mario and Luigi push it into the water and proceed to ride it down the river. Mario tells Luigi that he'll look out for any danger if Luigi steers. Luigi tells Mario that he should steer instead, because he's too afraid to open his eyes for what lies ahead. Just then, the two of them are assaulted by Birdoroo Eggs, which they barely manage to dodge. Mario instructs Luigi to use his paddle to escape to the other side of the river, but they aren't aware of the fact that Kangaroo Koopa and his Koopa Troopas are there. Kangaroo Koopa is surprised to see that Mario and Luigi made it this far, but he orders the Koopa Troopas to assault the brothers with boomerangs. Ducking under the boomerangs, Mario exclaims that they at least found Kangaroo Koopa, but Luigi points out that if the boomerangs don't hit them, the Birdoroo Eggs will. Mario tells him that they needn't worry about the attacks, and should instead worry about the rapids that they soon reach. Luigi then cries that they'll probably crash onto some rocks.
Back in the town, the crocodiles have chewed up the bottom half of the general store. Princess Toadstool tells the others that she hopes Mario and Luigi will soon return with the Magic Statue. The mayor then points out that the crocodiles are preparing a barbeque, which Toad states will be them. Princess Toadstool assures them that Mario and Luigi are doing everything they can.
Meanwhile, Luigi alerts Mario that they're nearly about to crash into a large rock up ahead. Watching from the shore, Kangaroo Koopa figures that Mario and Luigi are done for, and laughs to himself. Luigi concludes that they won't survive, but Mario gets an idea; he bends his plumber's helper into a boomerang-shape, which he refers to as a "plumberang". Mario throws his plumberang at some vines, which are then returned to himself and Luigi. Swinging across the vines, Mario and Luigi escape from the river, and avoid crashing into the rocks. On safe ground again, Mario and Luigi continue on their quest.
In the town, the crocodiles are still eating away at the general store. Toad comments that if he only knew how dangerous things were going to get, he'd have gone with Mario and Luigi instead. Princess Toadstool points out that the crocodiles are close to reaching them, so the mayor suggests that they all take refuge in the branches of a nearby tree. The crocodiles notice them, so they forget about chewing away at the store, and start chewing the trunk of the tree, which is also home to a koala bear. Princess Toadstool points out that Mario and Luigi need to get back with the Magic Statue soon, or there won't be anything left to get back to at all.
Meanwhile, Luigi complains to Mario for loosing Kangaroo Koopa's trail, which they need in order to find him. Suddenly, a stampede of crocodiles approaches Mario and Luigi, who avoid it by hiding behind a bush. Once the crocodiles pass, Mario realizes that they had been scared off for some reason. Luigi wonders what the crocodiles could've been scared of, which makes Mario come to the conclusion that they were fleeing from Kangaroo Koopa because of the Magic Statue. Luigi comments that they still can't find Kangaroo Koopa because they lost his trail, but Mario points out that if they follow the footprints of the crocodiles in reverse, they'll be led directly to him.
Mario and Luigi soon find Kangaroo Koopa sleeping next to the Magic Statue in a cave. Mario decides to just grab the Magic Statue, since Kangaroo Koopa probably won't notice them. After Mario grabs the statue, Luigi trips on a rock, waking Kangaroo Koopa. Kangaroo Koopa chases Mario and Luigi through Down Under Land, demanding for them to give him back the Magic Statue. Luigi slows down to let Kangaroo Koopa pass him, and Mario tosses the statue over Kangaroo Koopa's head for him to catch. Luigi throws the statue back over to Mario, and the two of them find themselves playing a game of "Koopa in the Middle".
Mario, Luigi and Kangaroo Koopa soon find themselves back in the town, where the mere prescence of the Magic Statue scares off any crocodiles that are near it. Mario approaches the nearly-chewed up tree, and tosses the Magic Statue up to Princess Toadstool. Princess Toadstool jumps down from the tree with the Magic Statue, and places it back on its pedestal. Asking for the Magic Statue to protect the town again, she kisses it, and it emits its power over the entire town, causing all the crocodiles to flee. Luigi points out that he and Mario are right in the crocodiles' path, but Toad throws a lasso in their direction, which they use to swing over to the base of the tree.
As Luigi comments that things had gotten close, Mario directs everyone's attention over to Kangaroo Koopa, who the crocodiles have now targeted and proceed to chase out of the town. Everyone in the town laughs at Kangaroo Koopa's defeat, and the mayor congratulates Mario and Luigi for their efforts. Mario suggests to him that they should throw a pizza on the barbie to celebrate.
Animation and continuity errors