Dr. Wily used Ra Moon to create Snake Man, and joined his growing army of Robot Masters in the Lanfront Ruins. Snake Man also appeared in Sonic the Hedgehog Issue 250 of the Worlds Collide crossover arc. In it, he fought Vector the Crocodile and was pummeled by the latter, with the crocodilian Mobian telling the Robot Master that he was "a disgrace to reptiles everywhere."
Because of Ra Moon's involvement in creating Snake Man, Snake Man aligned himself with Ra Moon after it took over. Snake Man also uncovered Mega Man and Break Man's plan to use a less guarded passage to reach the Temple of the Moon via one of his Search Snakes, with him and Needle Man being dispatched to ambush them in the tunnel. Rush managed to spot one of his Search Snakes, although Mega Man dismissed it. Snake Man then fell under direct remote control of Ra Moon and attacked Mega Man before being pinned to the wall by the Blue Bomber with Needle Cannon, having copied the weapon from Needle Man earlier. He then has his main functions restored, although he also congratulates Mega Man for accomplishing an ambush on him in a sinister manner, suggesting he and Needle Man have no memory of their actions under Ra Moon's control. Snake Man, alongside his brothers, were repaired by Ra Moon and they faced off against Mega Man, Break Man, several of the original Light robots, and the original line of Wily Robot Masters, with Snake Man being defeated by Quick Man.
However, after Ra Moon was destroyed by Mega Man, Snake Man was freed from his control and helped his brothers and Break Man search for the rogue Shadow Man in order to convince him to rejoin Wily's army. After Shadow Man agreed to do so, they teleported back with him to continue building Wily's new fortress. Before doing so, however, Snake Man snidely questioned Break Man as to whether he thought that Mega Man and Roll would forgive him as quickly as the Wily Masters had forgiven Shadow Man his role as Ra Moon's willing servant. He and his brothers of the second line later attacked Gamma's unveiling to steal the Energy Elements, something Snake Man found particularly enjoyable.
In issue 41, Snake Man along with his line set up their residence with one of the stolen Energy Elements, on an artificial mining asteroid. Snake Man becomes the second Robot Master Mega Man and Rush travels to. As they traverse through his stage, Snake Man silently stalks them, thinking to himself about how can Mega Man be the Blue Bomber, the one who defeated sixteen other Robot Master's beforehand and destroyed Ra Moon, when to the reptilian robot he is nothing but a scared little robot boy, recalling the fact that even when Snake Man was disabled back at the Lanfront Ruins, Mega Man decided not to finish him off. As Mega Man and Rush enter his room he ambushed them, covering them in Search Snakes and lashing at them with his helmet tail. Mega Man retaliated by using the Top Spin which knocked the snakes off of them while sending the serpent robot master into a wall. Before Snake Man could catch a second wind, Mega Man fired several several shots into him while Rush ripped off his helmet tail. Snake Man then smiles as he realizes this is why Mega Man is the Blue Bomber, just as he is destroyed by a charged shot.
After being rebuilt in issue 49, he questions Dr. Light's statement that all of the robots of his line have industrial purposes built into them, and Dr. Light answers that he was originally designed for topographical surveying. Snake Man notes that he finds the offer intriguing, and decides to join the eight Robot Masters who opt to remain online. However, they were soon called upon to put their skills as war machines into action again, as Dr. Light called upon them to answer the threat of Sonic Man after the Light Numbers failed to defeat him. Joined by Quake Woman, Snake Man and his brothers attacked the Hedgehog turned member of the Roboticized Masters, but proved unable to defeat him. As such, Sonic Man was able to activate one of his master Sigma-1's Unity Engines, which worked with one set up by M'egga Man, the corrupted Mega Man, to fuse Earth together with Sonic's home planet.
Snake Man and his brothers thus found themselves forced into an alliance with the Freedom Fighters, joining forces to help civilians after some initial trepidation. After being joined by the cured Sonic and Mega Man, the Maverick Hunters, and Team Sticks, the group boarded the Freedom Fighters' Sky Patrol base in order to take the fight to Sigma. This eventually led to an aerial battle with Sigma's Mechaniloids and the Deadly Six over the Lost Hex, where the robotic members of the crew were eventually taken over by the aliens' technology-manipulating powers. Snake Man "apologized" as he was forced to attack Rotor the Walrus, though the Freedom Fighter noticed he seemed to be enjoying himself. Eventually the robots were freed thanks to the Egg-Wily Uppity Robot Scrambler Cannon, only to find themselves and their allies facing an army of time-cloned Mavericks. Fortunately, the heroes of Street Fighter arrived in company with Sticks the Badger to save the day, allowing the heroes to pursue the scattered Mavericks to various worlds.