Mega Man X: Command Mission moves away from the series' standard side-scrolling gameplay and into the realm of turn-based RPGs. Users lead a team of Maverick hunters tasked with restoring peace to Giga City, an artificial island where a rebellion has broken out. Leader Epsilon and his Maverick allies wreak havoc, fueled by the mysterious Power Metal mined on the island. Veteran hero X takes center stage in the game, forming alliances with other Reploids who share his mission. Users overcome various stages, fighting enemies and bosses. Character development plays a key role, allowing you to customize abilities and equipment for each team member.

Mega Man X: Command Mission introduces a distinctive combat system called the Cross Order System. This strategic element gives gamers the ability to unleash special and finishing attacks using Action Trigger and Final Strike. Action Trigger, unique to each hero, activates once per turn, and Final Strike delivers a powerful strike when enemies are weakened. Mastering this system is critical to overcoming difficult encounters. Offering a fresh RPG twist on the franchise's classic formula, the video game retains the series' core elements: challenging combat, memorable characters, and the fight for justice in a setting threatened by a robot uprising.