Command Mission is made like a traditional turn-based RPG. Each character has Life Energy and Weapon Energy which act as HP and MP respectively. Turn order and the manipulation of it is a critical component of the game’s battle mechanics. Weapon Energy can be used by both Sub-Weapons that each character possesses and Action Triggers (special attacks).
Hyper Mode is much like a limit break. Each character can enact a unique attack for massive damage. There are also optional Hyper Modes that can be obtained for X and Zero.
One unique component to the game is its Final Strike ability. Once the bad guys on the field have lost over 75% of their life energy, Final Strike can begin in which all three characters can make an all-out attack against the enemies in an effort to defeat everyone.
Items work like most RPG item types. There are also typical defense commands, normal attacks, analyze to seek out information about the enemy, and run. Weapons, armor, and Force Metals can all be equipped for various attributes. One of the three characters can also be rotated out for an inactive character. The only downside to this mechanic is Weapon Energy is only replenished for active characters, so WE balancing is necessary with this aspect.
In 22XX AD, a new substance known as Force Metal is extracted from the debris of a small meteorite. Technology based on the metal revolutionizes the field of Reploids and becomes a rare, sought-out commodity. High concentrations of the material is feared to cause Maverick status, but the metal is too precious a thing to not utilize.
Our heroes X, Zero, and newcomer Shadow under the Commander Redips are given the mission to infiltrate Giga City, an island city built around the impact of the Force Metal meteor, once the initial team is assumed to be perished. A Maverick and Rebellion Army Commander named Epsilon has been able to overrun the city’s Force Metal factory and poses a great threat to Reploid advancement. The Maverick Hunter team follows energy readings to some ruins. A well-timed explosion separates the team, and X travels through the ruins alone for a time. In gathering information, the team finds out that Epsilon is in fact a high-performance Reploids completed at the factory. Three other high-performance units and eight combat units are found to have been constructed there.
The team finds Epsilon at the top of the ruins where he offers them a place on his team. After the team quickly refuses the offer, Shadow shows his true colors by turning his sword on Zero. X and Zero try to attack, but are stopped by Epsilon’s lieutenants. In the ensuing fight, Zero is thrown from the top of the building and X quickly escapes from his surrounding enemies.
X awakes to find himself in New Hope, a Resistance hideout that defends the city against Rebellion forces. They are led by Chief R and his assistant Aile (no connection to the Mega man ZX character of the same name). R was recently captured by the Rebellion, leaving the Resistance in tatters. X soon finds out that Giga City is a troubled people where the Rebellion forces have claimed that their cause is for the independence of the City against the outside world whom they call Federation agents.
After being notified to the authorities by a squealing Reploid, a bounty hunter named Spider fights X to fetch a pretty penny from the Rebellion forces. X runs into Aile who come to a mutual understanding. Aile gives X the ID necessary to seek out Chief R in the Governor’s precinct overrun by Rebellion forces and X fights his way to the Data Backup Room where the Chief is thought to be. The player sees Spider hashing out payment with Wild Jango, a Rebellion leader. Aile sacrifices his life in order to protect X. When Spider encounters X again and finds out of Aile’s sacrifice, he calls off the deal with Jango and changes sides.
X rescues Chief R from his captors, but not before Jango reveals that he’s taken Spider captive and set the entire building to self-destruct. X rushes to the Monitor Room and deactivates the sequence. He then is directed to the helipad on the roof in order to stop Jango from escaping. A hurt Spider comes to X’s aid and they defeat Jango, with the two heroes deciding to work together from now on.
After regaining the Resistance base, Chief R sends X and Spider to a Force Metal mine on Tianna Island that has been made into a POW camp by Rebellion forces. Nana, a system operator capable of restoring functionality to the base, is one of those held prisoner and the main objective of the mission. The hunters run into a powerful looking Reploid who claims to be Steel Massimo, a legendary hero. Despite being jumpy, he puts on an air of courage and joins their efforts to rescue the POWs. The Rebellion leader of the camp, Silver Horn, has been forcing Nana to maintain the security perimeter. When X and the rest come to where she is being hidden, she is surprised to see Massimo, as the records show him as having been executed.
Deeper in the prisons, Steel Massimo comes across the true hero of his armor, badly injured and on the verge of death. Having refused the Rebellion’s demands that he join, he remains an example of what happens to dissidents. The original hero entrusts his armor to the new occupant and deems him fit to uphold the name of Steel Massimo.
The three hunters return to Nana’s position only to find Silver Horn damaging her. After remarking about how he tore the real Steel Massimo limb from limb, the fighters attack Silver Horn and win. X and Spider reaffirm that Massimo has been able to live up to the name as the original hero requested, and the hunters bring Nana and the other prisoners back to their headquarters.
Chief R and Nana speak with X and the hunters about Dr. Gaudile, a genius who has remained neutral between the Rebellion and Resistance. X and the crew decide to visit his forest laboratory and try to persuade him to their side. After arriving at the laboratory and taking out some of the guards, Massimo notices a breeze and wonders if they are being followed. Unbeknownst to the heroes, they are being followed by a thief named Marino.
Marino comes across a young nurse Reploid sitting on a pedestal. Calling herself Cinnamon, she is confused by Marino’s asking about treasure. When she is asked where a Force Metal Generator may be, she explains that she is just such a device. Marino is convinced of this and decides to take Cinnamon with her. Back with the hunters, X and crew overhear Dr. Psyche threatening Dr. Gaudile on handing over Cinnamon for her Force Metal abilities. They both observe Marino taking Cinnamon on the monitors. Just then, X and the hunters enter as Dr. Psyche escapes to confront Marino. The two battle and Marino is badly damaged as a result. Cinnamon uses her abilities to heal the thief Reploid before she is captured by Dr .Psyche.
Once X and the others find an aching Marino, she argues to fight alongside the team which they begrudgingly agree to. The team catches up and wins against Dr. Psyche, but he hops into his Mad Nautilus battle armor to fight anew. X and crew are able to beat Psyche for good and bring Cinnamon back to Dr. Gaudile. The doctor maintains his neutrality in the matter, but Cinnamon surprisingly announces her desire to join the Resistance, joining the hunter team.
Commander Redips contacts X, telling him about a mysterious Reploid with a saber destroying the Ulfat Factory, a Reploid construction factory. X wonders whether this is his partner Zero and decides to investigate. In the factory, the group is surprised to meet not Zero, but Axl, another ally of X from past exploits. He also joins the group in an effort to find Zero, but little information can be gathered. Numerous Reploids are found slaughtered in the same saber-like fashion.
We then move to Zero arguing with a Rebellion Maverick, Mach Jentra, through a doorway. Zero is all but defeated when X and crew arrive to save him. Jentra escapes, and the factory alarm goes off announcing that “Duboar” has been completed. Resilient in their mission, the hunters track down Jentra and defeat him. In his last words, he states that without him, the Duboar will go berserk and destroy everything. Axl then realizes he can use his special ability to copy and Reploid to copy Mach Jentra and command the Duboar to cease. They dismantle Duboar and, reunited, return to the Resistance base.
Zero is angry with X for having partnered up with the Giga City Resistance, and takes off alone. Colonel Redips makes contact again to inform the team of Rebellion forces in the Gimialla Mine. As the team gets ready, X notices a bright light around the corner, and sees Spider, absent from the previous communication, appearing from the light. He shakes off the peculiarity and calls him to join the rest of the team.
As the team explore the mines, they are being watched and eventually run into their traitorous partner, Shadow who states he is looking for a “Supra Force Metal”. X is almost finished off, but Zero saves him at the last moment. This time, Shadow is defeated and Zero and X continue their conversation. A dying Shadow takes one last shot at Zero, but it is Spider who saves the hunter, killing Shadow in the process. A bit shaken from such an act, Spider earns Zero’s trust and they agree to work together.
Further on in the mines the hunters encounter the Rebellion Army Cadre, Incentas. He is ultimately defeated, but activates a self-destruct sequence. While trying to escape, Spider pins Incentas to a wall. X yells at Spider not to, but he throws the two of them into the energy barrier, destroying the both of them but also overriding the self-destruct and saving the crew.
Back at the base lamenting over Spider’s sacrifice, Commander Redips attempts to communicate but the signal has too much interference. Nana traces the distortion to the Onovan Desert and the crew decides to investigate despite Chief R’s warnings about the area. Finding the signal jammers, one of Epsilon’s lieutenant, Ferham, confronts the hunters mocking them about the quicksand around them. After attempts to escape and Ferham’s interference, the entire team is brought down by the quicksand into an underground facility.
After disabling the power grids of the facility, a Reploid named Botos confronts the hunters, remarking that he possesses a supreme amount of Supra Force Metal that X and the others cannot compete against. Despite these claims, he is defeated and escapes, but his Supra Force Metal is recovered. Back at the base, it is found that this Supra Force Metal is 10,000 times more powerful than regular Force Metal. The only place such metal could be constructed is found to be in the FM Refinement Plant, and the team heads out to that location.
Arriving at the Melda Ore Plant, the hunters find some mysterious objects being constructed. After consulting Dr. Gaudile, they conclude that the Rebellion is constructing a Force Metal missile. It is estimated that such a missile could cause half of the world’s Reploids to turn Maverick. Going deeper into the base, they run into and battle Botos again who hints about some keys needed to activate the missile. After escaping, Botos is tracked down and defeated yet again, but still escapes.
Coming to the central missile silo, Ferham confronts the hunters and is quickly defeated falling down a shaft. X and the crew realizes they need Ferham’s key, but Botos comes along and steals her key. The hunters come across Ferham who has been brutally beaten and they find out how Botos has gone completely Maverick. Botos dancing atop the missile criticizing Epsilon’s plan. A shadowy figure comes in front of Botos, making him react in terror. X and the hunters finally make it to the top of the missile to find Botos killed and the Supra Force Metal of the missile gone. Confused, the crew accepts this victory and goes back to base puzzled.
X finally makes contact with Commander Redips again calling for his planned attack on the found Rebellion base. The communication is cut short as the Central Tower is under attack by the Rebellion led by Cadre Scarface. He demands the return of the stolen Supra Force Metal and doesn’t believe X’s claim to not have the metal either. After a battle, X beats Scarface and he flees back to the Rebellion base.
Finalizing the location of the Rebellion base, X and Zero head out to the base’s location in the worst part of Giga City. The hunters go through various levels of security, they reach Epsilon’s elite guard and finally Epsilon. After some heated words, X fires at Epsilon, but Scarface takes the shots for his leader. Scarface argues for his rematch, and Epsilon allows it. Scarface is now defeated for good.
Epsilon now challenges the hunters as they stand, and after a lengthy fight, he is finally defeated. As he falls, he explains that he and his people had little choice in what they were doing as the Federation labeled them as Mavericks. Epsilon falls and X recovers the Supra Force Metal. Commander Redips appears behind the hunters and congratulates them on a job well done. X gives him the Supra Force Metal and is told that a transport will be prepared for their departure from Giga City.
As the team is on the helipad about to leave, Chief R is suddenly shot and killed and the area turns into chaos. X and the other hunters are accused of the murder and flee the scene. Redips makes an announcement to the people of Giga City stating that X is the killer, claiming he and his partners desired the Supra Force Metal for himself.
Realizing they were used, the hunters make their way to Redips’ stronghold to clear up being framed. To their surprise, they run into copies of former Rebellion leaders such as Wild Jango. X, Zero, and Axl share concern over whether or not any copy chips exist within the city, but continue on anyways. After defeating all the past bosses and one new encounter, the team finally makes it to the control center where Redips resides.
Redips explains his desire for total power and how Epsilon and the Rebellion Army was all a convenient setup so that he could possess the Supra Force Metal. X calls Redips a Maverick and the team fights the Commander. In defeat, Redips reveals that he is in fact also Spider. He is a Reploid with the same shape-changing abilities that Axl possesses, and posed as an ally of X’s this entire time. He escapes and leaves the hunters with this revelation.
After more chasing, X and the team finally finds Redips who has now combined with the Supra Force Metal to become an unimaginable power. Redips makes a similar argument to Sigma’s about how what is and is not Maverick will be decided by the future rather than Maverick hunters. The hunters are ultimately defeated by Redips’ powered up form. Suddenly, Ferham grabs the Supra Force Metal and tries to remove it. Redips is too powerful and overcomes her attempt. This distraction has given the hunters the opportunity to launch a second attack in which they finally succeed.
Ferham claims the Supra Force Metal and says that she will care for the metal so that no one will ever use it for such a purpose again, sacrificing herself in the explosion the metal makes in the Earth’s atmosphere. The last we see of our heroes, they are headed down to Earth, questioning whether what they have done was right or not.