Unlike the action-platformers of the Mega Man X series, Command Mission is a turn-based RPG. The game follows a narrative that forces the player to go to the different stages in order, which abandons the stage select feature of many Mega Man X games. The action is split between a field screen and a battle screen, with the player always in the center of the field of view and with a map of the surrounding area in the bottom-right hand corner of the screen. Player spend their time in one of the situations described below. The hub area linked to Central Tower. From here, players transfer to the different Adventure Stages. They can visit previously completed Adventure Stages, as well as ones vital to progressing through the story. Similar to other Mega Man X games, stages are spread around Giga City, which have to be cleared to progress through the story. Most of the time, the adventure stages are "empty", with enemies appearing randomly throughout the level as with traditional RPGs.
Throughout the game, the player may come across abandoned robots. Collecting them enables the player to deploy robots to Adventure Stages, where they can then search for money, information, data or rare items. Some robots may require special parts in order to be used. As with many RPGs, characters or enemies can be induced to enter different states of affliction that may affect their performance during battle. These status effects can all be healed by "Cure One," or "Cure All" except "DOA". Some names were changed due to the fact the characters are machines. The game features the appearance of Force Metals, special alloys from meteorites that fell from outer space. Reploids and robots equipped with Force Metals gain special abilities, however, the energy that these metals exude may have unwanted side effects if the character is overloaded past force metal tolerance. X and his companions can equip these Force Metals, which can be made from special recipes collected from Deployment Missions. However, they can only equip a certain number of Force Metals. They give Reploids special abilities. Exceeding the amount they can equip may lead to them becoming Maverick, which results in them starting battle with random afflictions including but not limited to the above. Finally, some Force Metals may cancel out the side-effects when equipped.
There are a few differences between the GameCube and PlayStation 2 versions of the game. The GameCube version makes use of the Nintendo GameCube Game Boy Advance Cable, in which players can connect a Game Boy Advance (GBA) to the GameCube, enabling the use of a special radar function to find secret items. A radar screen appears on the GBA screen, showing the immediate area around the player, the direction the player is facing and the location of any hidden items.[5] The PlayStation 2 version features an unlockable demo of Mega Man X8 instead. The frequency of enemy encounters is higher in the GameCube version. Also, if a player takes too many turns to defeat an enemy, they experience penalties far quicker in the GameCube version than in the PlayStation 2 version.
