Bionic Commando is a platform game in which the player controls Ladd, whose mission is to rescue Super Joe and to stop the Albatros project.[6] The game begins on an overworld map, where, Starting at Area 0, players can move Ladd's helicopter to any connected Area on the map in a nonlinear fashion. Each time Ladd's helicopter moves, the enemy ground vehicles will also move. Once the helicopter reaches its destination without crossing over the path of an enemy vehicle, the player can choose to "descend" and play that area or to "transfer" to a different Area.[7]: 7–9  If the helicopter is intercepted by an enemy vehicle, then Ladd must engage the enemy in an overhead shooter level similar to Capcom's Commando. Ladd, armed with a weapon and his grappling hook that he can swing around in a circle to deflect bullets and enemies, must defeat the enemy soldiers and reach the end of the stage. These are the only stages where the player can earn a continue.[6]
When Ladd descends into an Area, the player must choose which equipment to take along,[7]: 10–12  and is then dropped into a sidescrolling platforming level. There, the player must first find one or multiple Communications Rooms - where the player can communicate with allies or wiretap enemy conversations - and then proceed each Area's Computer Room, where a boss will be guarding the computer core the player must destroy to clear the Area. Ladd cannot jump, so the player must use Ladd's weapons and his bionic arm to defeat enemies and navigate platforms and obstacles. Players can extend his bionic arm overhead, directly in front, and above at a 45-degree angle, and can grapple to higher platforms, swing across chasms, and pick up items. Additional equipment such as weapons, protective gear, and communications devices can be found by clearing Areas or finding them in levels, some of which are vital to progressing further in the game. In addition to the regular "combat areas", there are also safe "neutral areas"; non-hostile zones where Ladd can gain additional information from allied and enemy soldiers and find items. If Ladd fires his weapon in any neutral area, an alarm sounds, and all soldiers will become hostile to Ladd.[6]