- Maniac mode
Successfully complete the game on the Expert difficulty setting to unlock Maniac mode.

- Boss Battle mode
Successfully complete Boss Survival mode to unlock Boss Battle mode.

- Mega Man Antique mini-game
Successfully complete the game on the Beginner or Expert difficulty setting to unlock the Mega Man Antique mini-game.

- Disable game progression
After the event where Master Albert shows his true intentions, you will be presented with four missions. Successfully complete The Highway, The Scrapyard, and The Control Center mission. After completing those three missions, skip the fourth, and go back to Hunter's Camp. Go all the way to the basketball goal, and open the way to the Quarry. Successfully complete the mission, and you will end up at the entrance of the Quarry. You will not be able to transform back to Model A or any of the transformations until you take the fourth mission you skipped. The transformation will be accessible during the mission. Successfully complete the mission, and the area you completed will be opened. However, the events that occurred in the Quarry will be gone, and you will not be able to go any further in the game.

- Expert mode
Successfully complete the game on the Standard difficulty setting to unlock the Expert difficulty setting.

- Boss Survival mode
Successfully complete the game with both characters to unlock Boss Survival mode.

- Secret Model A
Successfully complete the game with all 24 medals collected from the Bosses. Then, begin a new game. Get item 'A' and use it to unlock Secret Model A.

- Advent Quiz mini-game
Successfully complete the game to unlock the Advent Quiz mini-game.