Soon after the two rogue bionics and a wounded Lt. Magdalene escaped, Spencer was arrested by the FSA and sentenced to be executed for his treason. Returning to the present, Gibson releases Spencer on the condition that he assist the FSA against the threat to Ascension City. When given this ultimatum in exchange for his freedom, Spencer initially turns it down, but Gibson tells him he has knowledge of Spencer's missing wife. As Spencer progresses through Ascension City, he discovers information on Project Vulture, a super weapon being sought after by the terrorists. Spencer is ordered to retrieve the item before the Bio-Reign terrorists can. After finally gaining access to the item, he is betrayed by Joe who reveals himself as the leader of Bio-Reign. Joe has also enlisted the help of Gottfried Groeder, a character introduced in "Bionic Commando Rearmed". Joe reveals that Spencer's wife never left, and alludes to the concept that she is actually part of Spencer's bionic arm. According to Super Joe, in order for bionics to work perfectly, they have to sync with their host on both an emotional and physical level. In this case, Spencer's wife was the perfect candidate. After this revelation, Spencer hastens his pursuit after Joe who activates Project Vulture before Spencer reaches him. Magdalene tries to stall Super Joe, now in a Bio-Mech suit, but she is killed while Spencer is forced to helplessly watch. In a fierce mid-air battle, Spencer kills Joe and ultimately stops Project Vulture. He falls back into the hole of The Vault from which he, Joe and the vultures had ascended earlier. In the epilogue a brief conversation in Morse code is shown between the sniper (Thomas Clarke) who'd been following Spencer, and an unknown party. The first message reports that the Vault had been occupied and the Vulture Sentry System had been "disabled" before requesting further instructions. While the coded reply was not decrypted from Morse code for the audience (encrypted message is in German once decrypted), it apparently reveals the following declaration in response: "Execution of Phase Two Prepared. Activate Project Albatros [sic]." A comic book tie-in was written by Andy Diggle, with Colin Wilson providing the art. In the weeks leading up to the title's release, every Wednesday a new page was posted on the game's website. These single pages were collected in a thirty-five page comic, which was offered as a bonus for pre-ordering the title.