Two months after the previous game, a spaceship emitting energy similar to the Dark Elf has crashed. Both Neo Arcadia and the Resistance set off to investigate, only for them to meet a powerful Reploid, Omega, and its mysterious creator, Dr. Weil. Dr. Weil is a war criminal from a hundred years ago, but he was absolved of his crimes by none other than a resurrected Copy-X. Copy-X resumes command of Neo Arcadia, relieving Harpuia and the other Guardians of their duty, and instates Dr. Weil as his new military advisor. Dr. Weil then challenges the Resistance (and Zero specifically) to a race on who gets to the Dark Elf first.
This game introduces new collectible chips and a new weapon, the tonfa-like Recoil Rod.
This game provides examples of:
- Back from the Dead: Dr. Weil, being an expert in cloning, manages to bring back Copy-X as well as three of the Zero 1 bosses as part of his plans.
- Big Bad: Dr. Weil, who manages to usurp control of Neo Arcadia's government from Harpuia and later, Copy-X.
- Brainwashed and Crazy:
- The Eight Gentle Judges, when turned into Weil's Numbers, lose their benevolent natures and become nothing more than Weil's obedient enforcers, forcing Zero to cut them down.
- Omega, when fused with the Dark Elf, can cause other Reploids to become influenced under Weil's Mind Control, making them turn on humans as well as on Zero and Ciel.
- Co-Dragons: Copy-X Mark II, the Baby Elves, and Omega to Dr. Weil. The first is a figurehead put in place by Dr. Weil who takes command of Neo Arcadia from Harpuia. The second are convinced by Dr. Weil into helping him find their mother (The Dark Elf), and agree by helping him stop Zero. The third is Weil's most powerful minion, and the one capable of pulling off his Evil Plan in the first place.
- Cyberspace: Part of the gameplay, supposedly caused by the arrival of Omega. Entering it will cause some certain Cyber-elves in your possession (marked with "A") to activate at once, making you more powerful; it's Awesome, but Impractical, however, because 1) you can't get Secret Disks in Cyberspace, 2) entering it will cut some precious points off your score, 3) you'll eventually have to exit it before the stage's finish, so don't expect it to be useful on bosses. The sole exception to all of these rules is in the penultimate level, as only by entering Cyberspace can you fight Phantom, who's harder than the actual boss of the level (the Baby Elves) and said difficulty is likely why the mission score doesn't dock points as a result. Speaking of Phantom, he implies that cyberspace is a mix of Magical Database and a place where A.I.s of dead Reploids and cyber-elves go.
- Disc-One Final Boss: Copy-X Mark II is fought at the two-thirds mark of the game, and his death kicks the final stage of Weil's plans into high-gear.
- Dragon-in-Chief: While Weil is undoubtedly the Big Bad by having set the game's events into motion, Omega is the biggest threat that Zero faces, and the one that initiates Weil's Evil Plan. To drive it home, Omega's defeat spells the utter ruin of Weil's Evil Plan for 3.
- Elevator Action Sequence: When you get to the elevator, many mooks will come to get you. Oh, and a miniboss, too.
- Foreshadowing: Omega's first form bears some resemblance to Zero's classic design, most notably the spiky protrusions on the sides of his helmet and a long, flowing strand of hair reminiscent of Zero's ponytail.
- Fusion Dance: Omega absorbs the Dark Elf midway into the game, changing his armor from white to gold and bringing out his full potential.
- Hellevator: The Giant Elevator. You take a massive elevator deep into the Earth to fight a boss who's based off Cerberus.
- Legacy Boss Battle: Taking a secret detour in the second fortress stage will take you to a teleporter. Go inside, and you'll meet Phantom from the first game, or rather his "ghost" since he sacrificed himself. Defeat him and you'll get the Infinity Plus One Foot Chip.
- Locked Out of the Fight: The Guardians only show up to aid Zero after he defeats all three of the Final Boss' forms.
- Pet the Dog: During the intro level, Harpuia has his forces spare Zero's search party under the excuse that he has more pressing matters to attemd to.
- Puppet King: Copy-X Mark II to Dr. Weil, something pretty much everyone but Copy-X can see until X told him to his face that Weil and Omega left him to die fighting Zero.
- Riding the Bomb: The latter half of a mission, including the level's Boss Battle, takes place inside a missile as it was launched towards an unsuspecting target.
- Recurring Boss: Both Omega and the Baby Elves are fought in two battles. The former is the Warm-Up Boss and Final Boss, while the latter are fought at the first third mark and the penultimate boss.
- Rule of Symbolism: The low-orbit spaceship that Omega was sealed away in is shaped like a sword. It's a literal Sword of Damocles hanging over Neo Arcadia.
- Series Fauxnale: This was meant to be the final game.
- Star Scraper: The Neo Arcadia Tower used to be a space elevator connecting Earth and the Moon. It doesn't go quite that far any more, thanks to the Maverick Wars, but its top floor is still high enough for the curvature of the Earth to be visible.
- Tomato in the Mirror: Subverted, and how; near the end of the game, Weil finally reveals what's been hinted at for most of the game: that this series' Zero is Zero's mind inhabiting a newer, inferior version of his body, and that his original (insanely powerful and powerfully insane) body is being piloted by Omega; a puppet mind under Weil's control. For anyone else, having to essentially fight yourself would give you at least a moment of pause, right? Zero does not give a single robotic crap, and even with his inferior body, he annihilates Omega—and his old body—with complete conviction.
- Wham Line: The Reveal before the final boss reveals his true form.Dr. Weil: "Hehehehehe! Excellent, Zero! Your power is extraordinary, for a fake."
- You Have Outlived Your Usefulness: Ultimately, Copy-X Mark II is nothing more than a figurehead for Dr. Weil who is disposed of once he's no longer of use to the latter and already facing defeat at the hands of Zero. In a rage, Copy-X tries to go One-Winged Angel to get his revenge on both Zero and Weil, only to put the final nail in his own coffin by triggering the self-destruct Weil put inside his body.