Bionic Commando takes place sometime in the late 1980s and centers on two warring states: the Federation and the Empire. Federation Forces discover top secret documents about "Albatros", an unfinished project developed by the Empire's predecessor, the "Badds" (also known as the "Nazz"[5]: 4 or Nazis in the Japanese version). Imperial leader Generalissimo Killt decides to complete the project himself. Upon learning the Empire's plot, the Federation sends in its national hero, Super Joe (the main character from the 1985 Capcom game Commando[6]) to infiltrate the Empire, but he is captured. The Federation then sends in a second operative named Ladd to rescue him and to uncover the secret behind the Albatros project.[5]: 4 [4] Ladd is a member of the FF (Double Force) Battalion, a team of commandos specially trained to use wired guns to infiltrate enemy bases.[3]: 4
Gameplay begins as Ladd starts in Area 1, in which he is told that the first several areas, already infiltrated by Federation troops, have communication devices and rooms that can be used to stay in contact with the Federation and for wiretapping to gain intelligence from the Empire. Upon reaching Area 3, Ladd finds through enemy intelligence that Super Joe has been transported to the Imperial "disposal area", which a Federation spy later confirms. However, upon reaching the disposal area, an Imperial commander tells Ladd that Super Joe has been transported elsewhere. Eventually, Ladd locates and rescues Super Joe from a POW camp, who informs Ladd that the Albatros project is a powerful laser cannon the Badds were unable to complete. However, the one person vital to the project's completion, Master-D (Hitler), is dead, and Generalissimo Killt has been unsuccessfully trying to resurrect him. Super Joe tells Ladd that they must stop Killt before he succeeds, and he asks Ladd to accompany him to the Imperial base located in Area 12.
When Ladd reaches the Imperial base, Super Joe tells him to break the power system in order to release two power barriers that are guarding the incomplete project. After doing so, Super Joe tells Ladd to defeat Killt and escape while he goes to destroy the base's power source. When Ladd reaches Killt's chamber, Killt boasts that the Albatros project has been completed without Master-D's help, turning off the device that would have resurrected him. As Killt is about to kill Ladd, electric shocks begin to occur around the holding tank containing Master-D's body, reviving Master-D and instantly killing Killt. Master-D then exits the tank and approaches Ladd, saying that he will use the Federation's forces to take over the world. Ladd vows to fight against Master-D, who calls Ladd a "damn fool" and unveils the Albatros. After destroying the Albatros, Ladd encounters a dying comrade named Hal, who gives Ladd a bazooka and tells him that Master-D is escaping and that he needs to shoot the bazooka into the cockpit of Master-D's escape chopper. Ladd uses his bionic arm to swing himself towards Master-D's escape chopper and fires the bazooka into the cockpit; upon doing so, Ladd screams: "Your number's up! Monster!" Then, in a series of slow-motion frames, the game shows Master-D's head explode.
The 60-second alarm inside the Imperial base sounds off. Ladd escapes, realizes that Super Joe is still inside, and runs back in to rescue him. The Federation's commander orders the full evacuation of the base. At the Federation base, troops surround Ladd and Super Joe to celebrate their victory. On August 2, 2010, an old Super Joe recalls the entire story and hopes that it will live on.
