From the Super Mario Wiki, the Mario encyclopedia
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The Floppy Disk is an item in the PC release of Mario's Time Machine. Within the game, it contains the final version of the game itself. Before it could be properly validated and shipped off, Bowser steals it (by tricking Don Lloyd into sending it to him) and then brings it to his Museum. However, it is not exhibited alongside every other stolen item, which is unique to it. It appears only after every other stolen item has been brought to its rightful owner; after the second-to-last item has been returned, the Floppy Disk suddenly appears in the same room as the Timulator, and Mario automatically picks it up in a cutscene. Mario then travels in time to Novato in 1994 to meet the game's developers. Andrew Iverson is worried that Bowser wants to prevent the game from ever existing so that he can travel back in time with impunity (though he is reassured when Mario says that he has the Floppy Disk), and Don Lloyd tells Mario that Bowser asked for the disk and tells him to bring it to David Grenewetzki immediately after realizing who Mario is (though at first, when Mario asks him about the disk, he matter-of-factly tells him it is a floppy disk). Eventually, Mario brings the Floppy Disk to Grenewetzki, who thanks him for helping them ship the game, and he leaves Novato to confront Bowser.