- : Use the direction pad to control each character and guide them through the stages. Press left or right to make them walk in either direction. Press down to make a character squat or to descend a staircase. Press up to climb staircases, and also to enter through doors.
- : Press the A button to jump up in the air. Each character will jump to their maximum height regardless of how long the jump button is held down.
- : Press the B button to perform an attack. Each character can attack again as soon as their initial attack animation ends. Most characters (but not all) can attack while walking.
- +: Hold up while pressing the A button to switch to the next available character. For a character to be available, they must have been rescued and still have health.
- +: Hold down while pressing the A button to toggle between a characters regular attack and their special weapon, provided they possess one. If you switch from a character with a special weapon to one who does not have one, their regular attack will be used.
- : Press the Start button to begin a new game, or to pause the action mid-game. Pausing the action brings up the status screen, where every character's health can be checked, along with your team's inventory.
- : Only used in the shooting stage for a one-player game, allows a player to toggle between flying the Vic Viper and TwinBee.
One or two players
When a new game begins, you are first asked if there will be one player or two. In a one player game, the player controls one character at a time, and may switch between any available characters. At the start of the game, this will only be Konami Man and Konami Lady until a first character is rescued. When the shooting stage is reached before the final stage of the game, the player must choose to pilot the Vic Viper or TwinBee at the start of the stage, but then may press Select to toggle between the two during play.
In a two player game, each player plays simultaneously, with player 1 in control of Konami Man and player 2 in control of Konami Lady. Neither player may switch characters until at least one other character is rescued. Then the players can switch to one of the available characters. When the shooting stage is reached, each player must choose which craft to enter and pilot, and they must stick with that craft until the shooting stage has ended.
Dr. Cinnamon's lab
After Dr. Cinnamon charges the player or players with the task of saving Konami World, the players find themselves inside Dr. Cinnamon's lab. There are three doors which a player can choose to enter for various purposes.
- The first door returns the player to Dr. Cinnamon's office. Inside, Dr. Cinnamon will restore the health of any rescued and living character. He cannot restore the health of a deceased character. However, he can point you to the man who can. When he is done restoring health, he will ask you if you would like to learn more about any particular character. You will then be presented with a list of characters that you can learn more about. At the very bottom of the list is the name "Simon." Selecting Simon will summon Dr. Cinnamon's brother Simon, who will ask you if there are any characters that you would like to resurrect. Say yes and choose the appropriate character from the list. Simon will restore a dead character to full health, but only for the price of 100 bullets. If you do not have enough bullets, he will be unable to bring the character back to life.
- Behind the second door, Pentarou the Penguin presents you with a choice of six stages to which you can be teleported. Once a stage is chosen, the player's character will stand on the teleporter, and Pentarou will throw of the switch, sending the character off to that stage with a zap of electricity. Other than selecting a stage to be teleported to, nothing else occurs behind this door.
- The third door remains locked until all six characters have been found and rescued. Once this occurs, the third door can be opened. Behind the door are the Vic Viper and TwinBee. A player must select one of these vehicles for their character to pilot. Once this is done, the vehicle launches and the shooting stage begins. Successful completion of the shooting stage results in landing on the final stage where the battle against the ultimate boss takes place.