Two months after the previous game, a spaceship that crashed only recently emits energy similar to the Dark Elf, which Zero, Ciel and a pair of resistance members set out to investigate.
This game introduces new collectible chips and a new weapon, the tonfa-like Recoil Rod.
This game provides examples of:
- 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. Except for Phantom, as you need to enter Cyberspace to even encounter him in the first place. Speaking of Phantom, he implies that cyberspace is a mix of Magical Database and a place where AIs of dead Reploids and cyber-elves go.
- Elevator Action Sequence: When you get to the elevator, many mooks will come to get you. Oh, and a miniboss, too.
- 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.
- 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.
- 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.
- Wham Line: The Reveal before the final boss reveals his true form:Dr. Weil: "Hehehehehe! Excellent, Zero! Your power is extraordinary, for a fake."