64 years ago, Sky Captain was created as an unbeatable war tactician by Prof. Gerald Robotnik under the command of the MAFIA. Gerald soon realized Sky Captain wasn't afraid of anything and he strived for perfection. During his first flight, he crashed and was taken back to the facility. Gerald would notice Sky Captain feeling some sort of worry for him. After (accidentally) shooting Maria's pet-rat, thinking it was just vermin, Gerald got angry and abandoned Sky Captain for weeks. Irritated at his creator missing, he attempts to move out of the harbour, hearing two people talk about his project being scrapped, which would have Sky Captain soon end up as scrap metal. Snapping, he goes on a complete rampage, murdering a hundred of people working in the facility before Gerald was able to deactivate him. Althrough Sky Captains "last words" would haunt him forever.
Requesting Sky Captain to be instantly scrapped, Gerald, still caring for Sky Captain somehow, had him taken to the Space Colony ARK, hiding him. Waiting almost 50 years for Gerald, Sky Captain grew sick and tired, losing any emotions he might have developed and broke out of the ARK, heading to Mobius to make the entire world his and show his power and bloodlust to anyone, so they may fear his name. Disguising as an innocent Mobian hologram, he gains the trust of most mobians, including the Freedom Fighters to then attack them with his full force.
Sky Captain, when in battle, uses abandoned buildings to build himself an own base, where he can link with it to generate Tank and Hoverjet units remotely. His base is his last line of defense. If destroyed, he will just be re-built in his base a few seconds after his apparent death, becoming a little tougher each time terminated. The only way to DEFEAT Sky Captain is to infiltrate his base and sabotage the control over his base.