- Joystick: Use the joystick to direct Super Joe throughout the enemy base. Super Joe can run to the left and to the right. He can also squat down to duck under enemy fire, or return fire at the enemy's legs. Pressing up instructs Joe to pull himself up to a ledge that he is hanging from, and it also influences the direction in which the grappling hook is fired.
- Gun: Press the gun button to fire the weapon that Joe is holding at the moment. He starts with a standard issue gun, but can upgrade to alternate weapons that appear on the battlefield, falling down in parachutes.
- Grappling Hook: If the grappling hook is pressed without the joystick, it will be launched in whatever direction Joe is facing. Use this to knock enemies backwards, or to grab items that are otherwise out of reach. Press the joystick up, or upward diagonally to send the grappling hook in those directions. Once you are connected to something, press the grappling hook button again to reel in the cable and pull yourself up.
- 1-2 Players: Press either button to begin a one or two player game.
In Bionic Commando, you control Super Joe, who is on a solo mission to take down an entire enemy force by infiltrating his way into their base, destroying a giant missile, and defeating the leader of the force. He only has two items at his disposal: his weapon and his grappling hook. While his weapon can help clear a path through the hoards of enemies that assault him and try to stop him in his tracks, it is the grappling hook that will help him reach higher destinations and progress deeper into the enemy's base.
Joe can use the grappling hook in a few different ways. He can use it to knock enemies away before they get close enough to kill him. He can use it to grab items that are too far away to collect. And most importantly, he can use the grappling hook to grab onto ledges or platforms high above him. Once hooked on, he can either use the hook to swing across gaps to opposite ledges, or he can use the hook to pull himself up to the higher surface and continue.
Despite these two items, Joe is ill equipped defensively. A single touch from an enemy or a bullet is enough to end Joe's career. If you have another life in reserve, another Joe will parachute down from the top of the screen. While he is parachuting, he is invulnerable to enemy attack, and you can press left or right to guide him as he falls. However, the screen will not scroll while you are parachuting. Press any button to remove the parachute and drop straight down. If Joe is killed with no extra lives left, the game is over, but you can insert another credit to continue you game from right where you left off.
Found inside crates that slowly drop on parachutes, you must open the crates to discover what they contain. While the first five items in the chart below only offer you a few hundreds of points, the two flashing medals offer bonuses well into the thousands.