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Is there any way to change the controls? I have a controller plugged in and it DOES work, but the controls are backwards. I would use Joy2Key but doesn't work because when a controller is recognized by the game, it disables keyboard.

you need the DoConfig program that comes packaged with the freeware version of Cave Story. put it in the folder with your install of this game and use it to set the controls to your liking.

sorry for the trouble, Cave Story basegame is really weird with controller; you could try pressing F5 so the game reads from keyboard

There is also DoConfig, I forgot if there are any options there that would help in this case