Jungle Land is a vast jungle located somewhere on Mushroom World. Miles of tropical trees make up the primary atmosphere of Jungle Land, along with rivers, ponds, and the occasional quicksand pit. Animals that live in Jungle Land include apes, lions, Shyguy Lions, Albatosses, Trouters and Fryguys. The ape couple June and Ward are two notable residents who live in a society populated by anthropomorphic primates. Fabled treasure hunter Indiana Joe also resides in another part of Jungle Land, where he lives in a hut built over small pond. Jungle Land is also home to the dreaded Temple of Koopa.
Mario, Luigi, Princess Toadstool and Toad initially travel through Jungle Land as a shortcut, but are soon ambushed by King Koopa and an Albatoss, which kidnaps Mario before he can catch King Koopa. Mario manages to escape from the Albatoss' grasp, but lands headfirst on the front porch of June and Ward's treehouse, causing him to lose his memory. Mario wakes up unable to remember who he is; June and Ward choose to raise him as their own child, rename him "Marzan", and teach him how to behave like an ape. After mingling with some of the local monkeys, Mario beats up a lion with his outfit all torn up, and proclaims himself "Marzan, King of the Jungle".
Luigi, Princess Toadstool and Toad mount a rescue attempt, with King Koopa ordering his Shyguys to attack. Their attacks lure the heroes into a river, where they are almost devoured by a school of hungry Trouters. Mario swings down on a vine and rescues them, but the trio is shocked when he fails to recognize them, and he leaves to return to his adoptive parents' home for dinner.
Luigi, Princess Toadstool and Toad follow Mario's trail of banana peels to his home, but before they can restore Mario's memory, King Koopa orders his Shyguys to chop down the entire tree. Mario single-handedly defeats the Shy Guys at first, only for Luigi to inadvertently restore his memory right; fortunately, Mario still manages to send King Koopa and his army packing.
Ages ago, King Koopa's great-great grandkoop travelled to Jungle Land, where he discovered the wish-fufilling Lost Mushroom. What he used the Lost Mushroom for remains unknown, but according to King Koopa, it was supposedly left to him. Before dying, his Great-Great Grandkoop built the Temple of Koopa to hide the Lost Mushroom from the rest of the world, where it remained for many years.
Treasure hunter Indiana Joe moved his base of operations to Jungle Land to search for lost treasure of all sorts, and soon learned of the location of each and everyone one of them, in addition to all shortcuts leading to them. However, many of these treasures have yet to be found.
One day, Mario, Luigi, Princess Toadstool and Toad return to Jungle Land in a hot air balloon, as they are hoping to get ahold of the Lost Mushroom before King Koopa does. After sabotage from an Albatoss, they soon find themselves sinking in a quicksand pond. Indiana Joe rescues them, and offers to lead them to the Lost Mushroom.
Kolonel von Koop, not knowing the location of the treasure, lets Indiana Joe lead the way and steals it once it is found, locking Mario and his friends up in a tree hut with a Shyguy Lion afterwards.
After taming the Shyguy Lion, the group finds Indiana Joe at home and convince him to help them fight Kolonel von Koop despite his Koopaphobia.
In the meantime, Kolonel von Koop uses the Lost Mushroom to wish for a castle made of solid gold, but it is soon stolen back by Mario. Accompanied by Indiana Joe, Mario's group fights off against and defeats Kolonel von Koop and the Koopa Pack. With Kolonel von Koop gone from Jungle Land for good, its citizens can now live in peace.