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  • Neutral dpad: Movement
  • A button: This is used for interacting with the environment in the overworld, such as talking to people and activating switches. In Battle, it is used to select and use Battlechips. In the main menu, it is used to confirm an order.
  • B button: Holding this down in the overworld lets you run. In the menu screen, it is used to cancel an order. In conversations, holding it down allows you to skip through conversations, and in battle, it controls the Megabuster.
  • L button: In the overworld, it is used to talk between Megaman and Lan. In Battle, it can either open up the custom screen when the Custom gauge is full, or can be used to try to escape battle.
  • R button: In the overworld it is used to Jack into the Cyberworld or Jack out into the Real world. In Battle, it is used to open the Custom menu when the Custom gauge is full, and check the info on a battlechip in the Custom menu.
  • Start button: Opens up the main menu in the overworld, and pauses the game in battle.
  • Select button: In the Custom Screen in battle, it can be used to glimpse at the field of play, to help strategize.