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The main "mode" of Mario Paint was painting, which was done in a relatively sophisticated image editor, considering the only control was a two-button mouse. The game came with built-in icons and lettering tools to assist players with poor drawing skills.
Another of the game's modes was a music composer. Different icons were used to represent different sound effects, like a Mario for a jumping noise or a ship for a clanking noise, which the player could place on a music staff to adjust pitch and timing. Some Mario Paint compositions could actually get quite complicated. Other things like 3/4 and 4/4 time, tempo, and looping could also be adjusted.
Images in the game could also be animated using a few other tools (an in-game walkthrough of the steps made it a snap). After animating a few frames for the animated portion, then drawing a path for it along a pre-drawn background (a small animation could be given a path for movement, or a large animation could just be left stationary), the process was complete and players could view the animation at different speeds with black bars at the top and bottom of the screen. They could also play music composed with the game's music composer.
Mario Paint also had an infamous minigame, the fly-swatting game. The player controlled a hand with a fly swatter, and had to swat down various types of flies as levels progressed. Later enemies included flying bombs and wasps with homing missiles, and every several levels a giant boss fly would appear. A high-ramping difficulty and addictive sound effects made this game the bane of many gamers' existences.
Mario Paint was followed by the Mario Artist series, for the 64DD.