In issue 42, it is revealed that over 20,000 years before he became Shadow Man he was part of an alien line of robots called Kuiper Droids that served Ra Moon and the Stardroids. When the Star Marshals attacked Ra Moon, Terra gave the Kuiper Droids orders to escort their master to safety, but they were all destroyed, except for Shadow Man, who manages to land on Earth with Ra Moon, but he goes offline. Shadow Man and Ra Moon's survival was enabled by the treachery of the Star Marshal known as Trio, who murdered his compatriot Quartet.
Several centuries later, Wily, Heat Man, and Quick Man discovered him in the Lanfront Ruins. He is shortly repaired and redesigned as Shadow Man by Wily and Ra Moon. Surprised to be functioning again, he is recruited into Wily's growing army, and sent with a squad that also included Quick Man, Flash Man, and Magnet Man to investigate a proximity alarm. Their search would turn up the original Robot Master, who joined their forces under the name Break Man.
Shadow Man is mentioned in Sonic the Hedgehog Issue 249 of the Worlds Collide arc, where Doctors Eggman and Wily decided to send both Shadow Man and another Shadow Man (the latter being a Roboticized Master) to confront Sonic and Mega Man, after some initial confusion as to which one they should send. Shadow Man is then stunned by Mega Man with the Chaos Cannon ability after the latter ambushed and took out the roboticized Shadow Man, resulting in Shadow Man's restored identity, Shadow the Hedgehog, attacking the helpless Robot Master and smashing him to bits.
Shadow Man soon returned, however, time-cloned by Eggman and Wily as part of their massive Robot Master army. During the battle, he faced off with Espio the Chameleon, the pair apparently recognizing each other as fellow ninja. After the Super Genesis Wave's effects were reversed by Mega Man, Shadow Man and the others were returned to their proper places in time and space. The Genesis Wave that had previously affected their world moved their timeline into its near future.
When Ra Moon began spreading its EM field across the world, Shadow Man assured his fellow Robot Masters that they would remain unharmed if they obeyed Ra Moon. In Mega Man issue 30, he and Quick Man observe Mega Man, Rush, Guts Man, Bomb Man, and Cut Man forming a truce with Wood Man, Air Man, and Crash Man from the bushes. Quick Man is not sure about the validity of Mega Man's claim about the damage Ra Moon's EM field is doing, especially since he overhears Wood Man saying Wily would not go to such extremes. However, Shadow Man attacks immediately, piercing Quick Man with a kunai for his hesitation before dashing out from cover. He proves to be a formidable opponent, severing Crash Man's drills from his arms, knocking Wood Man down, nearly killing Mega Man (if not for Rush) with his first volley of Shadow Blades, and dodging counterattacks with superhuman speed and reflexes (even catching a Rolling Cutter and Metal Blade simultaneously).
Shadow Man then proceeded to attack Mega Man, but Quick Man intervenes just in time, buying Mega Man enough time to copy the Crash Bomber from Crash Man's severed appendages. Shadow Man takes the opportunity to literally backstab Quick Man with his kunai, though even his ninja reflexes are too slow to dodge Mega Man's Crash Bomber. However, Shadow Man survived the blast, escaping into the jungle before he could be stopped. He later participated in the fight between Ra Moon's forces and Mega Man/Dr. Wily's forces. He was paralyzed by Flash Man's Time Stopper, with Flash Man ordering for someone to finish Shadow Man off while he's still pinned down, and he is taken down with Hyper Bomb, Leaf Shield and Air Shooter.
After Ra Moon is destroyed, he laments his master's death and escapes with a smoke bomb, swearing that they will pay for what they did. In issue 33, Shadow Man is seen running away from the rest of Wily's Robot Masters and Break Man. He is still loyal to Ra Moon, and when he sees Mega Man "desecrating" his master's grave in Mega Man #34, he tries to attack him, but is stopped by Break Man and the second generation of Wily Numbers. Appearing to have a Japanese warrior code, Shadow Man says that he failed his master and now has no purpose, and asks them to finish him. It turns out that they hunted Shadow Man down to get him to join Wily's side and to have a new purpose in life, which he decides to do.
Shadow Man and the other Robot Masters who served Ra Moon later appeared in issue 36 to steal the Energy Elements powering the giant robot Gamma as part of Wily's latest scheme. Dr. Light recognized the other Robot Masters as designs he and Wily had created together, so it is possible that Shadow Man's new design was likewise produced by the two doctors working in tandem.
In issue 42, Mega Man faces Shadow Man in an asteroid. During his fight with Mega Man, he recalled his past, and declared that he wouldn't let his master down again. However, despite a harrowing fight, he ultimately was felled by Top Man's special weapon and Rush, with him realizing he'll die alone for real. Afterwards, Mega Man recovers the Energy Element that was with him, and later has him rebuilt by Dr. Light. A moody Shadow Man stood in a corner as his brothers were brought back online, his behavior earning him a look from Needle Man. However, when offered the opportunity to be reprogrammed and given a new purpose, Shadow Man chose to do so rather than be shut down like Quick Man and several of the others.
Shadow Man and those Wily Numbers who chose to accept a new purpose in life were later called upon by Dr. Light to fulfill their old purpose as weapons, being sent along with Quake Woman to battle Sonic Man. Despite their skills and weaponry, the nine Robot Masters proved to be no match for the Roboticized Master, and it was only the arrival of Break Man that saved them from greater damage. As Sonic Man fulfilled the orders of his master Sigma-1, the Robot Masters' world was linked to that of the Freedom Fighters, and the two began merging together. After an uneasy first meeting, the two groups began working together, and were soon joined by the restored Sonic and Mega Man and two groups from alternate times and realities, the Maverick Hunters and Team Sticks. Together, the alliance boarded the Freedom Fightes' Sky Patrol base in order to take the fight to Sigma. The crew was unexpectedly joined by Eggman, Wily, and Xander Payne courtesy of the latter's ability to create Genesis Portals, and with the doctors' input the Sky Patrol set course for the Lost Hex. Along the way, Shadow Man approached his master and revealed that his desire for a new purpose was a sham, and that he remained loyal to Wily and intended to betray the others.
He and his teammates would soon face an army of Mechaniloids led by the Deadly Six, and made headway against them until the aliens used their strange powers to take control of Shadow Man and his fellow robots. Though still capable of speaking freely, their limbs would not obey them and they began attacking their organic teammates. Eventually, Wily and Eggman freed their robot allies from the Zeti's control, just in time for Sigma to resurrect a mass of Mavericks. After a brief fight, Shadow Man and Antoine D'Coolette traveled to the world of Golden Axe to recruit its heroes and prevent the Unity Engine implantation. Shadow Man returned and aided in the final boss battle against Sigma before Xander undid the events of the crossover.
Blue Shift/Red Shift
At some point, Wily reestablished contact with Shadow Man, who began working as Wily's spy and informant on the state of the rest of the world, including what his former Robot Masters were doing and retrieving Break Man to do grunt work. He was particularly dismayed by his brothers taking new lives, considering them traitors for turning their backs on Wily's goals.
Shadow Man appeared in Issue 25's strip, which asked the question "What's the Greatest Battle of the Crossover?" referring to the Worlds Collide crossover in which the issue takes place. He appeared alongside Espio the Chameleon the Chameleon facing off with Pirate Man and Captain Whisker as the answer: "Pirates vs. Ninja!"
- The Archie Comics series takes a number of liberties with Shadow Man's character, particularly in terms of his origin story. This was mainly done by moving the events of Super Adventure Rockman to between the games Mega Man 2 and Mega Man 3. As such, Shadow Man-previously described as an ancient robot found in an unknown set of ruins-is connected to Ra Moon, and the pair in turn are connected to the Stardroids and the Evil Robot (named Trio). Prior entries in the franchise indicated no such connection between these characters, other than that Shadow Man was revived by Ra Moon in Super Adventure Rockman.