The story begins with Rad Spencer, the titular Bionic Commando, being tasked with rescuing Commando's protagonist, Super Joe from the "Badds," an evil empire bent on world domination, lead by the terrorist fiend, Master D. Super Joe had been sent in to stop the Badds' top secret superweapon, dubbed "The Albatross." All contact with Super Joe was lost, and Rad was sent in to go get him back.
Capcom took a page from Mega Man by giving the player the ability to choose which levels to tackle in any order. Players are initially presented with an overhead map of the game, divided into 16 levels. Players make their way from point-to-point, choosing whether to dive into the level and fight off the Badds and collecting power-ups, or moving onto the next level in the quest to rescue Super Joe. Of course, some power-ups are required to progress through certain levels, while others simply make it easier to take out more of the Badds. For example, in one level, the player must have the rocket launcher to destroy a wall to proceed.
The weapons have a cost/benefit system. One gun has a wider shot, sacrificing range. The rocket launcher can cross the entire screen, regardless of obstacles, but has a slow rate of fire. The types of enemies in each level varies, so matching weapons to enemies is crucial to success. This system is in contrast to simply getting more powerful weapons progressively throughout the game. Any weapon is viable in the correct situation.
One type of collectible upgrade is the communicator. In many cases the player must communicate with FSA agents to proceed through the level, in order to do this, the player must have equipped the correct colored communicator for that level. Failure to do so could result in the inability to complete the level. In special communication rooms, the player has the option to communicate with FSA agents or wiretap BADD communication- provided they have brought the correct communicator. In some cases, communication with the FSA agent results in the opening of a mission critical door, hence without the communicator, the level could not be completed. In instances where the player is unable to complete the level, the player can choose to be extracted from the level without penalty to lives, continues or upgrades, but losing any progress in that level.
Once in the level, the game has a very similar look and feel to other Capcom platformers, like Mega Man, DuckTales, and Ghosts 'N Goblins. Like those games, Rad will have to climb up towers, cross spiked pits, and shoot his way through wave after wave of enemy en route to the stage's boss. However, he cannot jump; instead, Rad is armed with a bionic arm, which can cling to practically any surface, allowing him to swing his way across the level's hazards. While difficult to truly master, using the momentum from swinging quickly becomes second nature, though it's still pretty common to miss a crucial jump and fall to Rad's death. Being an old-school NES game, Bionic Commando doesn't forgive mistakes.
On the level select screen, enemy trucks patrol the roads. If Spencer's helicopter comes into contact with one of these, Spencer must navigate an isometric top-down perspective battle sequence. During these sequences, the Bionic Arm no longer provides the game's jumping mechanic, but springs in an AOE attack radius around Spencer, knocking back enemies and deflecting projectiles. Possibly to combat the difficulty of the game, continues can be collected by destroying trucks in these sequences.
In 2000, Bionic Commando received a sequel in the form of the Game Boy Colour game Bionic Commando: Elite Forces. However, the story of Elite Forces was entirely unrelated to the story of the original game, and just shared the concept of a side-scrolling war game starring a soldier with a grappling-hook arm. Much later, in 2009, it was followed by another sequel, this time continuing the story of the original game, simply called Bionic Commando. To help promote the new game, developer GRIN also released a remake of the original game, entitled Bionic Commando: ReArmed. Unfortunately, the general reception to the new Bionic Commando was mixed, although the ReArmed side project was rather well-received due to its nostalgia value. While no further "real" sequels in the franchise have come out since, a follow-up to ReArmed, Bionic Commando: ReArmed 2, was released in 2011.