- For further reading on Mega City outside of the "Worlds Collide" and "Worlds Unite" crossovers, check out Mega Man Monthly.
During the city-wide birthday celebration of its hero Mega Man, Mega City came under attack from the mysterious Break Man. While the city was evacuated by Dr. Lights original Robot Masters, Mega Man was left to chase down the offender and attack. Moments later, the city was hit by the second Genesis Wave. (FCDS: 2013)
After the wave faded out, the whole city had been moved forward in time, where it was still being protected by Mega Man and the robots of Light Labs, including former "Break Man", Proto Man, who was no longer working for Dr. Wily. Before long, the city was attacked by the Roboticized Masters - Tails Man, Knuckles Man, Shadow Man, and Rose Woman - when they attempted to steal a Chaos Emerald within a bank located in the city. Proto Man attempted to apprehend these new threats on his own, until Mega Man arrived to take over the battle as his brother retreated to have his injuries treated. During the battle, Mega Man is knocked over by a speeding blue blur, allowing the Roboticized Masters to escape through a warp ring to Mobius, with Mega Man chasing after. (MM: #24, SU: #51)
Soon after, Mega Man returned to the city through a warp ring opened by his father Dr. Light, this time with Sonic the Hedgehog in toe, fully intent on finishing the battle that had started on his world in the Green Hill Zone. Having had the home field advantage back home, Sonic was now at a disadvantage, being in an unfamiliar location, and with Mega Man's reinforcements to deal with. However, concern for the civilians prompted Mega Man to try and reason with Sonic, leading to the discovery that the pair had been tricked. They were then attacked by Tails Man on the orders of Dr. Wily and Dr. Eggman, but managed to restore him to normal. The heroes subsequently departed to Light Labs, and from there to the Skull Egg Zone to confront the villains. (StH: #248, MM: #25)
Super Mega Man later restored his reality to normal, returning Mega City to its proper place in time. Unfortunately, it would later be attacked as part of another interdimensional plot involving Drs. Eggman and Wily, though this time Sigma-1 was the mastermind behind the scheme. Seeking to obtain the power of Earth 20XX using his Unity Engines, Sigma sent Sonic Man to set one up in Mega City. The local police, the Light Robot Masters, Quake Woman, several of Wily's Robot Masters, and Break Man attempted to stop him, but proved to be no match for the corrupted Sonic the Hedgehog. The city was then caught up in the effects of the Unity Engines, fusing it with Mobius to create a Unified World. Among the results of this were the Robot Masters meeting the Knothole Freedom Fighters, as well as the destruction of the Mega City government building and the Letter of Gabriel along with everybody inside and aboard. However, the altered city-now fused with Mobotropolis-also served as the site of Sonic Man and M'egga Man's return to normal, and their joining an alliance of heroes that included their teammates, the Maverick Hunters, and Team Sticks. The alliance then departed from here in order to hunt down Sigma. (StH: #251, #273; WUB: MM; StH; #8; MM: #50)
- Mega City initially went unnamed in the Archie Mega Man series, that is, until the mayor officially had the city's name changed in honor of Mega Man. This was stated during the first half of MM#23, which wasn't printed in the Free Comic Book Day issue.