One year after the previous game, Zero is wandering the desert, fighting waves of Pantheons. Elsewhere, the three remaining members of the Four Guardians have taken over Neo Arcadia, with Harpuia as the leader.
The game reintroduced the EX-Skills Zero could use in the Mega Man X games. It also introduces the Form System, depending on what color Zero is, he fights differently.
This game provides examples of:
- Big Bad: Elpizo becomes this following the failure of Operation Righteous Strike, seeking to defeat Neo Arcadia with the power of the Dark Elf.
- But Thou Must!: Refusing to help Elpizo with Operation Righteous Strike near the beginning of the game simply ends the conversation. However, there is literally nothing else to do other than roll around the base, which Elpizo snarkily lampshades if you initially refuse. Later on, once the operation commences, the two navigators will take turns begging you to follow Elpizo until you accept.
- Brainwashed and Crazy: The Dark Elf's and Baby Elves' Mind Control abilities allow them to influence or take control of other Reploids, making them follow Elpizo's directives. The latter makes full use of this during the last few levels on several Resistance members, the Guardians, and the Boss Rush to delay Zero.
- Chromatic Arrangement: The remaining three of the Four Guardians: Harpuia is green, Fefnir is red and Leviathan is blue.
- Continuing is Painful: Dying knocks three points off of your mission score. This is perfectly fair. However, dying also removes any points you'd accumulated from destroying enemies. God forbid you try to perfect-run the final stage.
- Curb-Stomp Battle: Operation Righteous Strike, despite the massive preparations, is a massive failure thanks to the intervention of the surviving Four Guardians, who massacre the Resistance members effortlessly.
- Greater-Scope Villain: X reveals to Zero during the ending that the Dark Elf was corrupted by a man named Dr. Weil. That same person makes a speaking appearance during The Stinger, directing someone named Omega to begin acting.
- Halfway Plot Switch: The first half of the game has Zero taking care of missions for La Résistance, or, more specifically, for its new commander Elpizo, in preparation for his Operation Righeteous Strike. When the Operation turns out to be a disaster, Elpizo becomes the designated Big Bad of the game, and the second half is spent trying to find him, and stop him from his plans.
- Kill All Humans: This becomes Elpizo's plan towards the end of the game.
- Meta Twist: The mandatory Boss Rush has six rematches instead of the traditional eight, but that's not the biggest surprise. The real surprise is that one of those rematches is Kuwagust Anchus bringing his brother Herculious Anchus (from Zero 1) to tag-team against Zero.
- Mind Control: One of the abilities of the Dark Elf and Baby Elves is taking control of other Reploids and bending them to their will. Elpizo uses this to his full advantage to make them attack Zero instead of him.
- My Friends... and Zoidberg: The second set of missions pit Zero against the three still-living Guardians...and Burble Herkelot. Since Herkelot is a member of Phantom's squad and Non-Elemental just like him, they might have been compensating...
- One-Winged Angel: Aside from Elpizo gaining a Mechanical Abomination second form in the finale courtesy of the Dark Elf, there's also the Armed Phenomenons of the three surviving Four Guardians. Fefnir transforms into a dragon-shaped tank, Leviathan turns into a manta-shaped submarine, and Harpuia turns into a bird-shaped aircraft.
- "Pan Up to the Sky" Ending: The ending involves Zero looking up to the sky from Yggdrasil.
- Sealed Evil in a Can: The Dark Elf is revealed to be sealed inside the body of X towards the end of the game. It gets released thanks to Elpizo destroying the latter.
- The Stinger: At the end, Dr. Weil commands his creation Omega to act.
- With Great Power Comes Great Insanity: Elpizo begins losing more and more of his mind the more he unseals the Dark Elf. By the final level, he's nothing more than a screaming, rampaging Berserker completely under the Dark Elf's whim.
- You Are Too Late: In the latter half of the game, Zero is always one step behind Elpizo, whether due to being legitimately too late to stop Elpizo from getting what he wants in said level or the boss of the level decides he's a much more interesting target than some crazy rogue Resistance commander. In the final level, Zero manages to catch up with Elpizo, but is unfortunately too late to prevent the rogue Resistance commander from destroying X's body and releasing the Dark Elf, thanks to Elpizo trapping him in a force field.