The game takes place 100 Years after Sigma's defeat in the Mega Man X series. Ciel and a group of resistance soldiers are being chased by a group of Pantheons and Golems. They find Zero's body, who looks a lot different than he used to. Ciel sacrifices her Cyber-elf, Passy, who breaks the energy shield and brings Zero back to life. Zero must now fight against X, his former partner, who now oppresses Reploids.
The game is a platformer like the previous Mega Man games but introduces several new concepts, such as Cyber-elves, one-time helpers who can increase Zero's abilities and a rank system depending on how well Zero is performing.
This game provides examples of:
- Armies Are Evil: Zig-zagged with the Neo Arcadian Armed Forces. On one hand, they're committing ruthless genocide against reploids, complete with "retirement facilities". However, it's revealed over time that their leaders are only doing so because they've been ordered to by X, and also because they believe that the Resistance are terrorists intent on causing mayhem to the humans living in Neo Arcadia.
- Big Bad: X at first seems to be the one pulling the strings on Neo Arcadia. Then, towards the finale, it's revealed that the X in charge of Neo Arcadia is in fact, a copy, and that the real X is the mysterious Cyber Elf helping Zero and Ciel.
- Curb-Stomp Battle: The opening cutscene shows numerous Resistance members getting cut down by Neo Arcadian soldiers and Golems effortlessly.
- Elite Four: The Four Guardians, reploids made in X's image who all act as the leaders of Neo Arcadia's Armed Forces and X's Co-Dragons.
- Final Solution: Neo Arcadia subjects numerous reploids to death, complete with facilities engineered for mass killing.
- Giant Mook: The Golem, mass-produced mechaniloids deploid by Neo Arcadia to serve as security forces. One of them serves as the first boss of the game.
- Guide Dang It!: While the game gives you the basics on how to level up your weapons, it doesn't at all mention certain hidden mechanics to the leveling system. While each killed enemy gives a weapon experience points, what the game never tells you, or at least only vaguely hints at, is that there are separate experience bars for different attacks with the same weapon (i.e. the Z Saber gets different experience with the normal slash, the dashing slash, the jump slash, and the charged slash). For example, while typical leveling with the Z Saber follows getting the double slash, then triple slash, the charged slash, the faster charging charged slash, and then the aerial spin and/or rolling slash, investing into killing enemies with the jump slash or dashing slash over normal slashing can unlock the aerial spin slash and the rolling slash before ever getting the double slash. The Z Buster follows a similar pattern in that it's possible to unlock the second level of the Charged Attack before unlocking the four bullets upgrade simply by prioritizing killing enemies with the Charge Shot over regular shots.
- Hopeless Boss Fight: Subverted with the first boss. Your only weapon is the buster, which at this point can only do one point of damage at a time, and the boss's Mercy Invincibility makes it practically an exercise in futility. However, midway into the fight, X as a Cyber-elf will appear and grant Zero his Z-Saber, which will One-Hit Kill the boss. Notably, the fight is not technically hopeless before you gain the Saber—it's just an agonizing slog.
- Hub Level: The Resistance Base compared to the versions in the later games. If there's a virtual map of the game world, the base can be found in the proverbial center, and most mission areas can be accessed just by walking through the base.
- La Résistance: The Resistance, of course. They're mainly composed of Reploids who have fled Neo Arcadia to escape persecution and certain death.
- Rebel Leader: Ciel, a human scientist who is also the leader of the mainly reploid Resistance.
- Red Shirt Army: The Resistance, who are often on the business end of the much stronger Neo Arcadian Army.
- Sequence Breaking: Leviathan will talk about your fights with Harpuia and Fefnir, whether or not you've even met them.
- Wake-Up Call Boss: Aztec Falcon, the first real boss, is known for shocking the players who have been used to the previous Mega Man games. Not only do you have a severely limited moveset by the time you fight him (unless you've been grinding, you're probably going to fight Aztec Falcon without the ability to fully charge your buster or do a three-hit combo with the saber), but the boss is also timed: fail to defeat him fast enough and the resistance members will be crushed in the trash compactor.
- Wham Line: Perhaps not that shocking, but there's this exchange, leading right into the final segment of the game:Cyber-Elf X: "NOW GO. TERMINATE THAT COPY OF ME...TERMINATE WITH EXTREME PREJUDICE..."