Successfully complete the game and wait until the credits end.
Boss Battle Mode
To unlock Boss Battle Mode, beat Boss Survival Mode once through.
Boss Survival Mode
To unlock Boss Survival Mode, finish the game with both Grey and Ashe.
Disable game progression
After the event where Master Albert shows his true intentions, you will be presented with four missions. Complete the Highway, The Scrapyard, and The Control Center. 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. 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. 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 further in the game.
Expert Mode
To unlock Expert Mode, beat the game on normal difficulty.
Maniac Mode
Beat the game on Expert Mode.
Model A
Successfully complete the game after collecting all 24 medals after defeating the Bosses. Model A will eventually become available during your next game by using the item 'A' in your inventory.
Quiz and Minigames
To unlock Quiz Advent and Mega Man Minigames, beat the game once through with either character. Quiz Advent is a quiz game, while the other is an "old-school" imagining of ZX Advent.