The final game in the series to run on the SNES, X3 was released in late 1995 and 1996 and on the Playstation, Sega Saturn and PC. Because the franchise was moving from cartridge based systems to memory cards this game became the last to feature the iconic Mega Man grid password system to save the game state. Like Mega Man X2, this game also used the CX4 microchip for simple 3D graphics processing that produced simple vector polygons during game play.
This incarnation saw the typical enhancements to graphics and level design, but especially won over fans by allowing players to play as Zero or X. Zero became an option that players could call in during a level, but could only take a certain amount of damage. If Zero became too damaged, the outcome of the game is affected during the final cut scene. Unfortunately, players cannot fight bosses with Zero, but at a certain point in the game, players can actually get Zero's Z-Sabre for X.
In the previous X games, players could find hidden upgrade capsules that enhanced X's abilities. For this game only, a slight alteration to the upgrade system for X was added. Players could also find chip capsules which would enhance and upgrade an upgrade ability even further. While there are four chips to choose from and players are limited to choosing only one chip at a time, players can return to previous chip capsules and swap them out.
It is many years after the Reploid rebellion began by Sigma. X and Zero now enjoy a peaceful existence in a human and Reploid utopia that has been formed, thanks to the efforts a new super intelligent science reploid known as Dr. Doppler. The good doctor created a neuro inhibitor, a device which shuts down any reploid prior to them going Maverick, allowing technicians to repair the reploid and save lives. As a result, reploids united around Dr. Doppler at his lab and formed a city called DopplerTown. Unfortunately, the peace was not to last as without warning, all the Reploids in DopplerTown suddenly go Maverick and revolt. Led by Dr. Doppler, who himself went Maverick, the revolting mavericks attack the Maverick Hunter head quarters and X and Zero reunite to suppress the rebellion.