The Doctor Is In... Over His Head
Mario is rushing to the Mushroom Kingdom General Hospital, because he believes there is a plumbing emergency there, and he has enlisted Princess Toadstool to carry his tools for him (because Luigi is busy). However, upon arriving, they find out there's no plumbing emergency, to Mario's disappointment. But the scatterbrained Dr. Waldo Bloom remarks that there is indeed an emergency here - he needs a new research assistant, and he's decided to give Mario that position. Mario's not keen on the idea (nor being called Dr. Mario), but the Princess insists that he do so.
Dr. Bloom shows Mario and the Princess through the hospital, showing off the room where they cure Mushroom People and enemies alike (they make enemies sign a contract to be good, though as the Goomba in the room shows, it doesn't always work). Dr. Bloom then brings them to his laboratory, where he explains that he's recently discovered Viruses that have been multiplying ever since. He has put the original specimens under a giant microscope, and the multiples in a jar. Just then, the original Viruses break loose from their container and land inside the giant microscope. Mario uses his plunger to open it up, releasing the now human-sized Viruses, who introduce themselves as Chill (blue), Fever (red), and Weird (yellow). After inflicting their respective sicknesses of coldness, heat, and weirdness on Mario, the Princess, and Dr. Bloom, the three break loose their smaller kin and escape through a window.
Mario takes off after the Viruses, but not before Dr. Bloom lends him his coat (which literally turns Mario's hair brown). He soon catches up to them and tries to fend them off. Eventually, he finds a supply of Megavitamins that Dr. Bloom had stored in the coat's pockets and soon discovers that stacking Vitamins of a certain color on the same-colored Viruses eliminates them, so he proceeds to take out the Viruses. Afterwards, he returns to the hospital, only to find that Princess Toadstool, now in her nurse uniform, suggested Dr. Bloom to take up golf, and he's not returning to his duty until he's finished his game, though as Mario notes, that could take a very long time (Bloom has made 456 strokes and is still on the first hole). Peach suggests that Mario stick around on the job as the Mushroom Kingdom's doctor in addition to being a plumber, which he eventually agrees to.