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The first character that joins X is Spider, a Bounty Hunter with a gambling motif who at first is looking to collect on X's head. After seeing Aile's core, he joins X due to Aile being a former partner of his. When the party are attacked by Shadow, he takes a shot intended for Zero, ultimately convincing Zero to rejoin the party. Shortly after, when they are trapped by Incentas, Spider sacrifices himself to allow the party to escape...or does he? After the fight with Ferham, we see Botos being attacked by a mystery person, one who has the same voice as Spider...
- Voiced by: Nobutoshi Canna (JP), Jonathan Love (EN)
- Bounty Hunter: Is introduced coming after X for the bounty the Rebellion put on his head.
- Death Dealer: Uses cards loaded through the equivalent of internal duel disks, each with varying levels of potency. Has the slick and smooth personality to match, and his Hyper Mode is called Trickstar.
- Expy: Is one ultimately for Double, with both sharing many similarities. Seemingly a friend? Check. Hides his true form? Check. Is The Mole? Check. Is he a major villain in reality? Check. Has a Meaningful Name? Check.
- Heel–Face Turn: Has his after seeing Aile's ID since it turns out they're old friends. Then he turns out to be a Heel–Face Mole Playing Both Sides all along.
- The Lancer: Replaces Zero in this regard, since they're not on the same team for very long.
- Meaningful Name: There's a playing card game called "Spider Solitaire". It's also "Redips" spelled backwards.
- The Mole: He's actually Redips manipulating both sides to take ultimate power via the Supra metal.
- Smug Snake: Although slightly less when he joins the team.
- Taking the Bullet: Intercepts a shot from Shadow's Pulverizer Cannon which was aimed at Zero, which convinces Zero to forgo his misgivings about the Resistance and join the party.
- Taking You with Me: Does this to Incentas to ensure the escape of the other Hunters.
Steel Massimo is the name of two characters: a hero who refused to join the Rebellion and so was captured and tortured, and a player character who took up the real Massimo's armor and name. This second Massimo joins X and Spider when they infiltrate Tiana Camp in order to rescue Nana. What he lacks in courage he makes up in determination.
- Voiced by: Yasuhiko Kawazu (JP), Noah Umholtz (EN)
- All Love Is Unrequited: Has a crush on Marino. She doesn't rebuke him, but is simply unaware of his feelings.
- An Axe to Grind: Most if not all of his weapons are axes and lances.
- Berserk Button: Insulting the original Massimo."...feeble Massimo? FEEBLE MASSIMO?! You Sunnova-!"
- The Big Guy: His imposing frame is probably the reason why he's the resistance party member who appears most often in cutscenes after Zero and Axl steal the spotlight and Spider dies.
- El Cid Ploy: Starts out as a good-natured Fake Ultimate Hero (specifically an imitation and protégé-in-spirit of his own role model) and ultimately grows to become a genuine hero in his own right.
- Expy: He and the original Massimo seem to be a combined Expy of the titular protagonist of Maximo: Ghosts to Glory.
- Gentle Giant: Very kind and caring.
- Glass Cannon: Especially towards the latter half of the game, as he's weak to all three Elemental Powers. His high health combined with Force metals can help deal with this, though.
- Golden Supermode: His Glint Armor, which not only enhances his powers but also negates the elemental weakness, making him just as tough as he is strong.
- Interface Spoiler: A very, very minor one. When he joins your party, he's Level 1 despite having allegedly been fighting the Rebellion for quite some time. This is the players first hint that this Massimo isn't the original.
- No Name Given: His original name and identity is unknown.
A thief looking to steal the Force Metal Generator from Gaudille's lab; she ends up befiending the naive Cinnamon, who reveals that she has the Force Metal Generator built into her. Marino decides she has to "steal" Cinnamon, but gets attacked by Dr. Psyche. She then joins X's team, because the Cadre are stealing precious valuables she could be stealing!
- Voiced by: Mariko Suzuki (JP), Carol Anne Day (EN)
- Classy Cat-Burglar: She's known as a master thief. In fact in her introductory chapter she befriends Cinnamon at the same time as she's trying to steal her her Force Metal Generator.
- Fragile Speedster: She's already quick, but her Hyper Mode cranks up her speed to such an absurd degree that she can potentially get infinite turns until it runs out.
- Lovely Angels: Has this dynamic with Cinnamon.
- Nominal Hero: As stated above, her excuse for joining the team after Cinnamon convinces her isn't quite above board, and she does only half-heartedly promise to X that she'll try to stop stealing if you talk to her at Hunter Base after beating Epsilon.
- Stripperific: Her outfit is one of the most form-fitting in the game, and in her Quicksilver Hyper Mode becomes particularly revealing below the waist.
- Technicolor Ninja: Styles herself as a Reploid kunoichi, getting around Gaudile's lab through quickness and stealth and using ninja weapons such as shurikens and chakrams. Contrasts nicely with the samurai Zero.
A young reploid who lives a sheltered life in Doctor Gaudile's lab, created to house his Force Metal Generator invention. Although she's naive and shy, she's the one who convinces both Gaudile and Marino to join X against the Cadre because she wants to make her own decisions and help her new friends.
- Voiced by: Ai Nonaka (JP), Caitlynne Medrek (EN)
- Ascended Extra: She had an archetype based after her in Rockman Online, giving equal importance as the X, Zero, and Duo archetypes.
- Apologetic Attacker:"Sorry, but I did warn you."
- Barrier Maiden: Her Force Metal Generator and healing capabilities make her very valuable and coveted by all sides, or at least it seems that way at first. However, none of the Rebellion after Psyche really care about acquiring her, which they probably wouldn't given the actual force metal refinery they have as well as the existence of Supra-force metal, and while her healing trigger and metal forging capabilities do come in handy, the Resistance members clearly see her more as a person than as a tool.
- Cheerful Child: She appears to be foolishly naive once Marino comes to her to steal the Generator (which happens to be her), but is only really charmed by the thief because she senses goodness in Marino. After things get really bad with Psyche's attack on the lab, she's clearly wiser to the ways of the world, but usually maintains an optimistic and hopeful demeanor nonetheless.
- Combat Medic: Give her the Kitty Gloves and she'll hit just as hard as the others—and that's even after the nerf they got in the International editions to 16 power. The Japanese release, by comparison, had 66, effectively making Cinnamon able to hit almost as hard as Marino's Comet weapons, and that's before you take into account how the gloves can reduce enemy stats with each hit.
- Lovely Angels: Has this dynamic with Marino.
- The Medic: With her around, sub tanks aren't even necessary to heal her allies 100%. All it takes is her action trigger.
- Power Fist: Not usually clenched, but still effective.
- Power Gives You Wings: Her hair functions as this during her Angelic Aide healing action trigger.
- Tagalong Kid: Takes this role from the now-matured Axl.
- What Happened to the Mouse?: Her post-game whereabouts are the best kept secret out of everyone's.
- Zettai Ryouiki: Though it's not as easily recognizable as most examples due to the size of her reploid boots.
A platypus Reploid who developed the Force Metal Generator and built Cinnamon. He's determined to stay out of the conflict between X and the Cadre, but Cinnamon eventually convinces him to join the cause.
- Voiced by: Naoki Tatsuta (JP), Randall Wiebe (EN)
- Actual Pacifist: He refused to join the Resistance (nor especially the Rebellion) because he didn't want his inventions to be used for war. Cinnamon convinces him anyway.
- Always Chaotic Evil: Averted here; he is probably one of the only animal-type Reploids in the series that is not a maverick that you get to interact with.
- Overprotective Dad: Tried to say no to joining the Resistance in the war along with Cinnamon until she assured him she could handle it. This is understandable, though, since he created both Cinnamon and the Generator inside her, so for both significant and sentimental reasons he doesn't want her falling into the wrong hands.
- The Smart Guy: A force metal expert researcher with a mechanical nature laboratory who can build reploids and create force metal forging gems, yeap, he qualifies.
- We Used to Be Friends: Implied with Dr. Psyche.
The leader of the Resistance. He was initally held hostage by Wild Jango until X freed him, after which he assumed command and assisted the team with his clever strategies and deep knowledge of Giga City. He was killed when signaling the transport ship that was supposed to take the Hunters home opened fire. His pet bird still survives to the ending.
- Voiced by: Hideyuki Hori (JP), Ben Jeffery (EN)
- Mission Control: To Hunter Base.
- Pirate Parrot: Apparently it's for monitoring and information handling.
- Reasonable Authority Figure: Reserved yet prudent, the Resistance highly respects his strategic wisdom.
- Stealth Pun: See the mechaniloid bird on his shoulder? Think what his name sounds like.
- As a bonus, one of the sketches shows him with a peg leg as well.
- And the bird's name? O-M-8.
- Stuffed into the Fridge: Though the bird apparently survived and is standing with Nana.
A young computer specialist who worked at Central Tower before being kidnapped by Silver Horn and forced to work for him as a sys-op at his POW camp. Once X and his friends free her, she becomes the navigator for the team.
- Voiced by: Akemi Kanda (JP), Angie Beers (EN)
- Bridge Bunny: The team's navigator and Chief R's second in command.
- Brought to You by the Letter "S"/Seven Is Nana: Her chestplate features two 7's on it.
- Emotionless Girl: Forced to be this while at Tianna Camp.
- Mission Control: To Hunter Base.
- Spanner in the Works: Doesn't tip Silver Horn off about X and company when they get to her room, naturally due to the fact that he's holding her hostage, and they're there to rescue her and the other POW's.
- Suspiciously Similar Substitute: Easily for Alia, considering that Nana's role is almost identical to Alia's, not to mention that this is the only game since her introduction that Alia doesn't appear in.
A member of the resistance against the Rebellion Army, he was apparently a former partner of Spider's who was injured and lost the use of his legs, replacing them with a hover-wheelchair of sorts. After agreeing to work with X and giving him his ID (which means casually tearing it off of himself, since it was built onto him) he sacrifices himself to allow X to escape the endless number of PREONs converging on their location. Not to be confused with the Mega Man ZX protagonist with the same name.
- Voiced by: Masaya Takatsuka (JP), Scott Roberts (EN)
- Bounty Hunter: His previous occupation.
- Frozen Face: His mouth doesn't move when he talks in-game (the right-side image is concept art), although he does have one. Just how bad was that injury?
- Heroic Sacrifice: As stated above, sacrifices himself to stop the PREON mechaniloids converging in on him and X.
- Stupid Sacrifice: We all know that X could have taken those PREONS. It's possible that Aile simply didn't believe he was capable of any other contribution to the cause...
- We Hardly Knew Ye: His sacrifice takes place in the same scene he's introduced in.
The Rebellion Army
- Rebellion Cadres
The leader of the Rebellion Army. He was actually the result of secret Supra Force Metal experiments and was the only subject to not go Maverick or be destroyed for failure. Given extraordinary abilities thanks to the Supra Force Metal, he sought to give all reploids the same power to evolve beyond what humans had created them to be...whether they actually wanted it or not.
- Voiced by: Yukitoshi Hori (JP), Dave Pettitt (EN)
- Anti-Villain: Turns out to be this, believing that force is the only way to get people to listen to their ideal.
- Asskicking Equals Authority/Authority Equals Asskicking: The strongest member of the Rebellion is also their High Commander.
- Climax Boss: Closes out the Resistance-Rebellion struggle, but there's still more to go in the game.
- Death Equals Redemption: Implied in The Stinger, where it was stated that the Government posthumously cleared Epsilon of all charges of being a Maverick, instead transferring the charges onto Redips.
- Disc-One Final Boss: Unsurprising for a Mega Man X game, however The Man Behind the Man is not the one fans had come to expect...
- His goals are very similar to the goals of General from Mega Man X4.
- He's also got some things in common with Sigma. Visionary reploid, Greek letter name, ripped cloak (Mega Man X6), shoulder rods (Mega Man X7), Dave Pettitt's English version Badass Baritone (Mega Man X8)...reduced to a Disc-One Final Boss/Unwitting Pawn for a copy-generation reploid (also X8)...
- His appearance is akin to a large reploid version of Cloak.
- Meaningful Name: In mathematics, the symbol Epsilon represents the margin of error. Obviously, his creators knew how risky their Supra-force metal experiments were.
- Reasonable Authority Figure: Implied with the hierarchy of his rebellion: Most of the ones more prone to being maverick are placed at the bottom tier, and those who aren't maverick are at the top.
- Red Eyes, Take Warning: They add to the intimidation factor that makes him a…
- Scary Black Man: Big E here is the first black human type reploid in the series.
- Sequential Boss: The fight against him consists of two phases.
- Sole Survivor: It's stated that he was the only one of the Reploids who underwent Supra Force Metal testing that neither went Maverick from exposure nor was killed from it. This also acted as his motivation for exposing all Reploids to the Supra Force Metal, realizing that the results could be reproduced.
- Unwitting Pawn: To Redips.
- Well-Intentioned Extremist: Wants to advance the potential of Reploids, forced into taking the "by any means necessary" route due to being framed for Maverick.
- Your Terrorists Are Our Freedom Fighters: The Rebellion is basically the epitome of this, and he's the commander.
A member of the Rebellion Cadre, and Epsilon's right hand man. He's the most sympathetic of the Cadre, and first to make X question just how 'evil' they really are.
- Voiced by: Yasunori Masutani (JP), Corby Proctor (EN)
- Adaptive Ability: Is able to resist and counter any second consecutive melee or ranged attack.
- Anti-Villain: He's loyal to the antagonists but his methods and personality are far from those of a heel.
- Black Knight: Somewhat subverted, as his hard armor is a combination of yellow and orange. However, the rest of his attire is mostly black, he's every bit the Noble Demon, and according to the data for his chamber at Lagrano Ruins he's built to be a knight.
- The Dragon: To Epsilon.
- Gameplay and Story Segregation: The plot and dialogue played his first battle as a duel between him and X, even with other characters praising X for facing him alone, but in gameplay it was really a normal three-on-one battle.
- Good Scars, Evil Scars: Has a massive scar on one side of his face, hence the name.
- Noble Demon: He's incredibly loyal to Epsilon, even taking a fatal Charge Shot for him. Also…
- Never Hurt an Innocent: When he stormed Central Tower to challenge X to a fight, he only attacked the members of the resistance that attacked him first, and even went as far as to heal the ones he damaged.
- Senseless Sacrifice: He attempted to hold off the Maverick Hunters to buy time for Epsilon to escape, taking his life in the process. Didn't work.
- Undying Loyalty: To Epsilon and the Rebellion.
Another member of the Rebellion Cadre. She initially was the chief of security at the Force Metal Research Facility until Epsilon convinced her to join him. She seemed to share a tender relationship with Scarface, only giving him 'permission' to use her key.
- Voiced by: Yuka Koyama (JP), Onalea Gilbertson (EN)
- An Ice Person: Her elemental power, making her the opposite of fellow Rebellion high flyer Mach Jentra. That said, it's not all she's got to her.
- The Baroness: Sexpot personality type. Clearly enjoys flirting with Zero in chapters 7 and 8.
- Dominatrix: She even coos for Zero to come 'play with her' while she's whipping him.
- Doppelgänger Attack: It's called Crimson Shade, and it's even more potent than Zero's Heat Haze.
- Flight: Seems to be VTOL-based, in fact it's so good she's able to travel this way.
- Harping on About Harpies: Is based on this.
- High-Heel–Face Turn: And an example that's not turning against the group she was working with, but rather affirming that, while their goals are dangerous, their hearts are in the right place. It's the Treacherous Advisor on the Federation end that had them branded Maverick so he could take their goods and become a god with it that was the real bastard to worry about.
- Redemption Equals Heroic Sacrifice: Leaves the atmosphere with the Supra-Force metal after the final battle, blowing herself up with it so that it can never be used for harm again.
- Undying Loyalty: To the other Rebellion Cadres.
- Unexplained Recovery: Between chapter 8 and 10.
- Whip It Good: Her main weapon.
The last member of the Rebellion Cadre. Unlike his comrades, Botos talks big about the Cadre's cause but is actually a pompous coward only out for his own gain. When Ferham is defeated by X and his party, he rips her key from her body so he can steal the Supra Force Metal for himself. He's killed by an unknown assailant who seems to look very familiar…
- Voiced by: Kozo Shioya (JP), Tommy James (EN)
- Dirty Coward: Only fights his enemies when he thinks he's at an advantage, but should he find himself outgunned, he'll scour out a way to will run from his enemies.
- Doppleganger Spin: He relies on this heavily after losing his force metal and combat prowess.
- Fat Bastard: Full of greed and cowardice.
- "Get Back Here!" Boss: X spends a long time trying to catch up to him after their first battle. Of course, by this point Botos is too weak to be a proper boss...
- Gonk: Particularly when his mouth's open as it is in-game.
- Irony: He's Rewarded as a Traitor Deserves. Tried to manipulate the Rebellion in order to get his hands on all the Supra-Force Metal and the power that would come with it. His killer was doing the exact same thing, but was just better at it—and without even being in Epsilon's organization.
- Jerkass: As Ferham found out the hard way when she needed help.
- Not in This for Your Revolution: Is only hanging with the Rebellion so he can get his hands on Supra Metal, openly attacks a wounded Ferham for her metal and calls Epsilon and the Rebellion STUPID when he's on the verge of acquiring the warhead's metal scot free.
- Small Name, Big Ego: When he's in a situation he thinks he can handle, he is way too full of himself.
- Top-Heavy Guy: His midsection is so much bigger than his legs it's a wonder they can support it.
- Villain Decay: After his force metal is knocked out of him in his first boss battle, he stops being a threat to X's party and becomes an annoyance instead.
- Rebellion Army Operatives
A member of the Far Eastern Maverick Hunters who was sent to Giga City along with X and Zero. When he and Zero are split up from X, he betrays the Hunters and joins the Rebellion for power. He later returns, powered up by Supra Force Metal, in order to challenge X. Upon his defeat, he tries to fire a last ditch attack, but is defeated by Zero and Spider.
- Voiced by: Masaya Takatsuka (JP), Ryan Luhning (EN)
- Backpack Cannon: His long range weapon, and he is damn good with it.
- Expy: To several of the Dragons in the series: The most obvious is Vile, both being vicious, power-hungry former Maverick Hunter turned traitors with a Shoulder Cannon as one of their main weapons. Then there's Double, another psychopath with an energy Blade Below the Shoulder who shows a much nastier side of his personality when he's revealed to be playing for the other side. Finally, there's Dynamo, another rival of X and Zero who uses both an energy blaster and saber and worships Sigma much like how Shadow worships Epsilon.
- Face–Heel Turn: In the first chapter of the story.
- Interface Spoiler: Never officially joins the playable party through all of chapter 1.
- Laser Blade: His melee weapon, in contrast to Zero's Beam Sword.
- Mood Ring Eyes: Depending on his personality at the time. When he's trying/pretending to be a nice guy they're blue, but when he goes into power-hungry heel mode they go crimson.
- Obviously Evil: His name and appearance practically gave him away from jump.
- Slasher Smile: After turning on the Hunters.
A fleet-footed bobcat Reploid keeping Central Tower captive for the Rebellion at the time X drifts there from Lagrano Ruins. He also seems to be aware of Spider's reputation as a bounty hunter, even hiring him to eliminate X.
- Voiced by: Yasunori Masutani (JP), Gerald Matthews (EN)
- All Your Base Are Belong to Us: Pulled this on the Resistance before the start of the game.
- Not Me This Time: It is implied in the aftermath of his battle at Far East HQ that the "Wild Jango" that attacked Giga City, held Chief R hostage, and was fought by X and Spider was actually a Next-Generation Reploid mimicking him, possibly Redips.
- Panthera Awesome: Of the lynx variety.
- Shock and Awe: His elemental power which fuels nearly all his attacks.
- Wolverine Claws: Uses these for a running attack.
Silver Horn/Silver Horned
A hulking triceratops-type reploid who operates an undersea POW camp for the Rebellion Army. He seems to run the camp with an iron fist, and behaves in a very arrogant, drunk-with-power manner. Spider and X are sent to his camp to rescue the Resistance base operator Nana, the prisoner who incurs his wrath more than any other prisoner that he hasn't already dismembered…
- Voiced by: Daisuke Gori (JP), Bryon Close (EN)
- Expy: Of Flame Mammoth, elements aside.
- Fat Bastard: Nana and the original Massimo would not disagree.
- Hypocrite: The overhelming majority of his POWs hardly count as the "slimy vermin of the world" he says must bow to the Rebellion's power.
- Making a Splash: Uses water powers and can even induce a "splash" of sorts by stomping the ground and causing the water in his coliseum to burst up into a tidal wave.
- Sadist: Proves to be one when Nana is being held and coerced as captive to function as the Tianna Camp's systems operator, or else he would have the remaining prisoners held there executed.
- Would You Like to Hear How They Died?: Clearly, he loves his job a little too much. Especially for Massimo's taste.
A computational reploid who used to be a research partner to Professor Gaudile. He appears in Gaudile's laboratory first to try to convince Gaudile to join the Rebellion, then to wrest control of Gaudile's Force Metal Generator. Despite hinting that he knows of Epsilon's good intentions, he himself acts in an insane, power-hungry manner. Has an "evolved" form called Mad Nautilus, which looks like Exactly What It Says on the Tin.
- Voiced by: Kozo Shioya (JP), Roger Rhodes (EN)
- Everything's Squishier with Cephalopods: Mad Nautilus.
- Flunky Boss: One can't be blamed for thinking his support needles are more dangerous than he is at first.
- Mad Scientist: He's quite clearly insane.
- One-Winged Angel: Mad Nautilus.
- We Used to Be Friends: Implied with Gaudile.
Mach Jentra/Mach Gentler
A barn swallow type Reploid who, though native to Giga City, was sent back home by the Federation government to help out with peacekeeping before defecting to the Rebellion. He is in charge of the Ulfat Factory and its creation of PREONs via the computer at the core of the factory called Duboar. He's also the only one who can control Duboar, as the machine goes berserk in his absence.
- Voiced by: Masaya Takatsuka (JP), Tony Binns (EN)
- Flight: Courtesy of thrusters in his boots and on his back.
- Large Ham: Especially when he thinks he's winning.
- Mook Maker: Duboar. He controls it and seems to care about it to an extent.
- Playing with Fire: Considering he's running a volcanic factory, it only makes sense.
- Wicked Cultured: Has the personality of refined English gentleman, complete with the accent in the English version.
A member of the Rebellion Army. He's the boss guarding the Gimialla Mine where Supra-Force Metal is reported to have been found. However, it was all a trap to get X's party locked into the mine's command room, where he planned to destroy them either through battle or by pulling a Red. This led to Spider's sacrifice, a key event driving the events of the second half of the game…
- Voiced by: Daisuke Gori (JP), Roger Rhodes (EN)
- Barrier Change Boss: He uses all three and swaps between them.
- Convenient Color Change: His body energy and armor will both change colors depending on each elemental state. His default state, seen in the above image and cutscenes, features his electric state's yellow and sky blue body armor and his fire state's burning body energy.
- Multi-Armed and Dangerous: Especially with the Asura Knuckle.
- Multiple Head Case: Also has three separate heads, one to face forward for each elemental state. His default state features his yellow-framed brown Ra head, which he uses in his fire form.
- Xanatos Gambit: The introduction of high capacity Force Metal mining, combined with having to go through the Supra-Force-infused Shadow, was just about enough to draw the Resistance command team right into a lethal trap. It's only too bad he wasn't counting on the cowboy to be willing to risk it all so the others could pass…
A strange insane duck-styled Reploid working for the Rebellion as a hidden boss. Is apparently assigned to guard a certain treasure that could be useful to the heroes…
- Voiced by: ??? (JP), Roger Rhodes (EN)
- Bonus Boss: Defeating him nets Zero a new Hyper Mode: the Absolute Zero Armor!
- Cloudcuckoolander: Named his hammer and drill Naguru D and K-Ball respectively, considers them as actual mechaniloids, goes laughing mad when introduced, frequently spews non-sequiturs in battle.
- Elite Mook: Seems to be one of those to the Rebellion, if his talk about them assigning him to guard the armor and their insignia on his head are any indication.
PREONsA mass produced combat mechaniloid that acts as the Rebellion's main grunt units. They come in many different variations. They are mass produced by the mechaniloid Duboar.
- Mascot Mook: Essentially, given how abundant they are in this game.
- Shoot the Medic First: Not actually the best strategy with PREON Nurses, if you leave them alive at the end and defend instead of attacking them, they'll show their gratitude by healing you for free.
- Subverted that if you let them live they run away taking with them the EXP and money would earn if you did blow up..of course you can subvert it again by blowing them up after you get your free heal from them.
Far East HQ
The leader of the Far East Maverick Hunter HQ. He acts as X and Zero's commanding officer and oversees their infiltration into Giga City until signal jamming makes communication impossible. But when X and his team finally get all the Supra Force Metal from Epsilon and give it to Redips, he betrays them and labels them as traitors. He uses the SFM to declare himself a god and intends to rule over all reploids.
- Voiced by: Ryoichi Tanaka (JP), Michael Shepherd (EN)
- Big Bad: Out to rule the universe.
- Bling of War: Pretty much just another Expy of Colonel or Signas. Of course, it comes with a Commissar Cap.
- Evil Cannot Comprehend Good: He calls X and his friends Mavericks because he cannot understand their Power of Friendship.
- Evil All Along: Even Zero has to ask again what he and the others were fighting for.
- High-Altitude Battle: Great Redips is fought in a space station, to be exact.
- Hopeless Boss Fight: For the first half of the final battle.
- Ironic Echo: You know how he mentions that History will tell who is a maverick? Well, the Government pretty much answered that question in the stinger when they placed all of the charges against Epsilon against Redips.
- The Man Behind the Man: Manipulated the entire Rebellion war so he could fish them out and take their Supra metal.
- Mission Control: Operates as this, ostensibly from Far East HQ.
- Nice Job Fixing It, Villain!: Had he not shot Ferham in irritation with her attempt to pull off his Supra-Force Metal with the Healing Factor, she wouldn't have been able to do it and the Hunters would never have beaten him.
- Sdrawkcab Name: Purposefully misspelled as Rideps in the manual in order to put players off the scent.
- Treacherous Advisor: Guided the Hunters into basically destroying the only guys in his way all the while planning to dispose of them as "traitors" afterward.
- Your Princess Is in Another Castle: A particularly dickish example at that.
- Walking Spoiler: Can't really talk about him without giving much away.
A member of the Far East Maverick Hunters, completely loyal to Redips. When Redips reveals his plans, Dragoon attempts to defeat X's team but is himself defeated.
- Voiced by: ??? (JP), Gerald Matthews (EN)
- Blood Knight: His primary motivation for fighting X's team was because he wanted to see X's power with his own eyes.
- Giant Space Flea from Nowhere: He appears after the traditional Boss Rush in a random room before the Final Boss. None of the characters acknowledge his presence after he's defeated, either.
- Making a Splash: He is a seahorse, after all.
A Reploid hidden away in Tianna Camp, who calls herself the "Super Idol" and seems to be working on a dance routine. She becomes agitated upon being walked in on by the party, oblivious to the powerful item inside her room…
- Voiced by: ??? (JP), Carol Anne Day (EN)
- Bonus Boss: Defeating her nets X a new Hyper Mode—this game's version of the Ultimate Armor!
- Gender Bender: Not herself but Axl can morph into her after you beat her, which leads to some amusing implications.
- Lone Wolf Boss: There's no indication that she has anything to do with the Rebellion.
- Queen Mook: She's a boss version of a similar but rare female random encounter enemy.
- Regenerating Health: Both Rafflesian herself and the Belladonnas fully heal every turn, making a concentrated blitz necessary to take each one out.
- Wolfpack Boss: She and her Belladonnas are this because on top of their impressive power, they always come in threes—whether she's among them (her Tianna Camp boss battle) or not (the end of the Eternal Forest "Path of the Strong" at Gaudile's lab).
The Ninetails Clan
A group of dangerous criminal reploids who fight using a sort of robotic chi instead of elemental powers, sealed away in the lowest shaft area of Central Tower, which can only be accessed by a key acquired after defeating the game. They all look alike, and all have nine tail spaces on their backs, though how many tails are actually there varies between each one by name in escalating order from the first member encountered, Onetail, to the leader, Ninetails. The most powerful enemy in the game by far, including all the other Tails and other hidden bosses, Ninetails seems to be the one they're all based off of.
- Voiced by: Hideyuki Hori (JP), Corby Proctor (EN)
- All Your Powers Combined: Aside from the Annihilator Hadoken, Puncture Arrows, and Ninetails' Nine Fragments, every other ability and attack they have is bitten off previous enemies in the game.
- Blood Knight: All we know is Ninetails is a dangerous criminal and he and the other Tails' reason for fighting the heroes when encountered boils down to "I challenge you to a fight."
- Bonus Bosses: Can only be fought after the end of the game.
- Doppelgänger Spin: A possible interpretation of the Tails is that Ninetails is the only original one and the others are all shadow clones of him similar to what Botos does in chapter 8. This is based on the vast majority of their powers being borrowed from all the other enemies in the game, the fact that they all sound and look alike except for the tail spaces on their backs, and the Resistance troops referring to "A savagely strong prisoner", hinting at only one known captive held down at Shaft 999F.
- Fixed Damage Attack: Ninetails' Nine Fragments does 999 damage 9 times to one character, for a total of 8991 damage!
- Fire/Ice/Lightning: One of only a handful of enemies able to employ all three elements with equal lethality while not being weak to any of them.
- Kitsune: The android version. By the time one gets to Fivetails it shouldn't take much to figure out that the trail stops at Ninetails.
- Lone Wolf Boss: Like Rafflesian, they don't seem to be in with the Rebellion.
- Shotoclones: Again, especially Ninetails. Exhibit A would be…
- Shout-Out: Their Annihilator Hadoken, which Axl sadly doesn't copy in his morph of him, instead copying a set damage attack of the last of them.
- Suicide Attack: The Self Destruct technique of Fivetails and Sixtails. Fivetails will just use SOS to summon a fresh Fivetails. Sixtails only does it once after ten turns have passed and ends the battle when he Self-Destructs, but if he does, you lose the sub tank part and figure tokens he was carrying and can't obtain 100% Completion.