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Mario, Luigi, Princess Toadstool and Toad have traveled to the Oriental city of Sayonara, and are seeking out a martial arts master by the name of Misaki, whom they believe has the skills needed to save the Mushroom Kingdom. While traveling down a street, a paper lantern falls before the group, who soon find themselves surrounded by several Ninjis. Before Mario's group can make a break for it, Karate Koopa announces that they can't escape. Mario attempts to fight against an attacking Ninji, but he misses, and instead gets tossed around by the Ninji. Two Ninjis then corner Luigi, one of which kicks him into a basket full of fish.
Karate Koopa then orders the Ninjis to tie up Princess Toadstool and Toad, stating that he intends on selling them into slavery. The Ninjis proceed to do so, and Princess Toadstool argues that Karate Koopa won't get away with his plan. Koopa then directs her attention over to Mario who is knocked-out, implying that he can't be stopped. At that moment, Misaki makes his entrance by leaping out from behind a building, and states that he will stop Karate Koopa. Misaki starts to beat up several Ninjis singlehandedly, and this prompts Koopa into leaving with Princess Toadstool and Toad on a Ninji-drawn rickshaw.
Misaki goes on to defeat the rest of the Ninjis by himself, which also impresses Mario and Luigi. With the Ninjis all gone, Mario approaches Misaki, asking if he can teach them to fight like him. Misaki comments that no one can fight like him, but agrees to help, as they are all enemies of Karate Koopa's.
Misaki brings Mario and Luigi to his dojo, where the two plumbers have donned karate outfits and will be referred to (from this point on) as Mario-San and Luigi-San. Misaki proceeds to karate chop a brick in half with no trouble, the mere sight of which startles Luigi-San. Mario-San questions as to when they'll eat lunch, but Misaki resorts to slamming him against the floor, reminding him to stay focused, and not to let his mind stray. Luigi then comments that Mario was thinking about pasta, like he normally does. Misaki then instructs Mario to hit him with a bo staff, and succeeds in not only grabbing the bo, but tossing Mario onto the floor again as well. Luigi fears that they'll never be able to defeat Karate Koopa with their lack of skill, and Misaki decides to try and teach them a different fighting style that will work better for them.
Now outside of his dojo, Misaki agrees to teach Mario-San and Luigi-San Plumb Fu, the most dangerous form of karate ever invented. Mario asks as to what Plumb Fu even is, and Misaki explains that it a fighting style passed down from plumber fathers to their plumber sons in succession. Mario-San and Luigi-San take a immediate liking to Plumb Fu, as Mario uses a bo staff resembling a double-sided plunger to knock Misaki to the ground. After quickly getting back on his feet, Misaki orders Luigi to snatch a washer from his hand. While twirling a nunchaku made from two small chained-together pipes, Luigi does so, which prompts Misaki into teaching them the secrets of Plumb Fu.
Meanwhile, at Karate Koopa's pagoda, Koopa has tied Princess Toadstool and Toad to a column. The Princess demands to be released, and warns Koopa that Mario and Luigi will come after him. Toad argues that they'll beat up Koopa, but Karate Koopa tells Toad that if Mario and Luigi have any brains, they'll stay away from his place. Looking out of a window through binoculars, Karate Koopa concludes that Mario and Luigi don't have any brains, as he spots them approaching his pagoda with Misaki.
Walking towards Karate Koopa's pagoda, Misaki commends Mario-San and Luigi-San for passing his Plumb Fu test, and asks if they're ready to face Karate Koopa. After Luigi asks if he can think about the option for a few years, a net falls onto the three fighters, trapping them. Karate Koopa gloats about his capture, and after some brief arguing with Misaki, he soon has them chained to a boulder, which he is ready to launch into the ocean from a catapult. Koopa then releases the catapult, and sends the boulder flying into the water. Watching from inside the pagoda, Princess Toadstool points out that Mario and Luigi are sunk, as well as themselves.
Having landed on the ocean floor, Mario, Luigi and Misaki struggle to break free from the boulder. Misaki attempts to karate chop the chain, but discovers that Karate Koopa made it karate-proof. Mario figures that the chain probably isn't Plumb Fu proof, and cuts it with a hacksaw. Misaki congratulates Mario, and the trio proceeds to walk across the ocean floor back to dry land. On their way, a school of Trouters surround the group, and they struggle to fight them off using Plumb Fu punches and kicks. Luigi then points out a drainpipe that they can escape through, and they swim towards it. After nearly being attacked by the Trouters, the fighters enter the drainpipe, which Luigi seals by closing the grating.
Mario-San, Luigi-San and Misaki climb out of a manhole near the entrance to Karate Koopa's pagoda, where Misaki discovers Mario's and Luigi's weapons on the ground, which they had lost upon being captured by Karate Koopa previously. The group then enters the pagoda, but they have no idea as to where they should start looking. Ninjis proceed to jump out from behind various walls, and prepare to attack Mario's group. Misaki fights off the Ninjis that attack him without a sweat, while Luigi cowers as two Ninjis surround him. As Misaki attacks more Ninjis, Mario proceeds to attack some of them with his plunger staff. Swallowing his fear, Luigi assists Mario and Misaki into fighting off more Ninjis with his nunchaku.
Meanwhile, Karate Koopa is eating at a table in another room, accompanied by Mouser, Tryclyde and a Koopa Troopa, where he announces that the bidding for Princess Toadstool and Toad will soon begin, and encourages them to drink up their Koopa-Kola. While Toad whines about Koopa's plot to Princess Toadstool, the princess tells him that she's been working on loosening her rope, and succeeds in untying herself. After untying Toad, the two of them run off, but Karate Koopa gives chase and catches both of them.
Princess Toadstool cries for help, and Mario-San manages to hear her while fighting the rest of the Ninjis alongside Luigi-San and Misaki. Mario insists that they all go to save Princess Toadstool, but Misaki tells him to go alone, while he and Luigi take out the Ninjis. Luigi, however, isn't too fond of letting Mario leave him. Mario runs over to the room where Karate Koopa is, and demands for him to let his captives go free. Koopa drops Princess Toadstool and Toad, then proceeds into pulling out his nunchaku. Mario blocks Koopa's attacks with his plunger bo, until Koopa succeeds in wrapping up Mario's bo with his nunchaku, and tosses him aside.
Mario gets back on his feet, and stops Koopa from performing a kick attack by blocking him with his plunger bo. Taking advantage of the situation, Mario tosses Karate Koopa aside, while Toad cheers him on. Mario then charges at Koopa and knocks him on his back with his plunger bo, before tossing him onto the horn of a decorative sculpture. Koopa's clothes get stuck on the horn, causing him to dangle from it. Mario informs Koopa that he's been defeated, which prompts him into making his getaway by tossing a Magical Potion and creating a Warp Zone, through which he escapes. Luigi-San and Misaki then arrive, and Misaki announces that they finally defeated all of the Ninjis. Luigi is relieved as Mario already took care of Karate Koopa for him.
After returning to Misaki's dojo, Mario's group has sat down to enjoy a Japanese meal, when Misaki announces that he would like to thank Mario-San and Luigi-San for mastering Plumb Fu, and decides to award them with black belts. Having already put on a few extra pounds, Mario takes another bite of his food, which Luigi takes away from him, his weight gains. Misaki then presents Luigi with his black belt, and he proceeds to put his on. Mario puts on his black belt, but it isn't long enough to properly go around his extended waistline, and snaps off. Mario then requests for a second black belt, which Toad points out that he should receive for eating and everybody laughs.
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