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  • Alternative Character Interpretation:
    • Spider's entire premise. Fans will seem forever divided on whether or not Redips was actually Spider all along, or killed the real Spider halfway through the game and assumed his identity. There is evidence to support both theories, and, seeing as how a sequel to this is rather unlikely to happen any time soon, there may ultimately be no final answers.
    • Additionally, the nature of Redips's plan. Was he aware of the Supra-Force Metal in Giga City and seeking to obtain it from the very start? Or did he learn about it as Spider and decide to hunt it down then? If so, why was he masquerading as Spider in the first place?
    • The entire Rebellion Army: initially they seem to be a bunch of greedy, power-hungry sociopaths who cruelly oppress and subjugate everyone in Giga City — until you find that a few of their members (namely the Cadre) are surprisingly fair and honorable people, and the fact that they're the project of unethical experiments as well as being manipulated by The Man Behind the Man. Even Ferham, the seemingly sadomasochistic Baroness, has a genuinely tender moment with a comrade. Their leader might have a point that using force really might be the only way for a group of Reploids to be heard.
  • Angst Dissonance: This can occur throughout Chapter 2 regarding the death of Aile. So, this random guy X has never met before shows up. He gives X his ID and then performs a Heroic Sacrifice to keep some guards at bay for X... okay. Then for the rest of the chapter, every single character incessantly bashes the player over the head about Aile's greatness. By the end of the chapter, X makes some sappy remarks about how Aile brought them all together, while the player is left confused and utterly unattached to this character that was introduced and died in the same cutscene.
    • Happens a little bit with Ferham too. By the time she performs her own Heroic Sacrifice, Ferham has merely been a cool villain with a Heel–Face Turn at the end of the game. X really shouldn't have that much of an emotional attachment to her, but still lets out an anguished Big "NO!" when she leaps off the Orbital Elevator.
  • Angst? What Angst?: Chief R, the leader of the Resistance, is mercilessly gunned down by Redips' orders. The other characters really don't seem too shaken up about it, despite him being one of their most trusted colleagues.
  • Awesome Music: While Command Mission does have a weaker soundtrack out of the X series, having more mellow techno beats befitting a sci-fi RPG, it still has a handful of rocking tracks. Some stand-outs include Fight, X!, Standby - Zero, Boss Battle, and Redips 3rd Movement.
  • Big-Lipped Alligator Moment: Hippopressor. It's a giant multicolored hippopotamus that bursts through a wall apropos of nothing at the end of the intro stage. It does not speak and so cannot offer any explanation for its presence and it is never spoken of again after the boss fight. Zero sums it up best:
    Zero: Who the heck is this?!
  • Complete Monster: The Reploid Silver Horn sticks out as a sadist on a perpetual power trip lacking in any of his Rebellion Army compatriots' redeeming qualities. Warden of the Tianna POW camp, Silver Horn viciously kills many dissenting Reploids himself during the Rebellion's takeover of Giga City, personally torturing the famed hero Steel Massimo into a limbless, barely-living heap and keeping his mangled body underneath the camp. Forcing the Navigator Reploid Nana into acting as a sysop for the camp under the threat of executing all of the POWs, Silver Horn's response when he's finally confronted is to gleefully reminisce on his torture and eventual murder of Steel Massimo to his successor and revealing his ideals that the weak only exist to serve the strong.
  • Critical Dissonance: While most critics found the game a run-of-the-mill JRPG that's So Okay, It's Average at best, the X fandom mostly looks past this and cherishes it for fleshing out new characters and ideas in the world of Giga City. Some of the fan-favorite characters have even appeared as mainstays alongside the usual cast, such as the inclusion of Massimo, Cinnamon, Marino, and Ferham in Mega Man X DiVE. The change of pace to a JRPG was also appreciated.
  • Ensemble Dark Horse: Nana gets a surprising amount of love from fans despite her somewhat removed role in the story.
  • Epileptic Trees: Speculation on whether Redips was always Spider, or if Redips killed the real Spider and replaced him at one point. There is in-game support for both arguments.
  • Fanon Discontinuity: Some players like to ignore the final chapter and the Ass Pull plot twists it makes, particularly in regards to Spider and Redips, preferring to believe the game ended with Epsilon's defeat.
  • Fridge Brilliance:
    • Massimo's complete weakness to Elemental Powers, thus making him a Glass Cannon / The Load after the halfway point in the game, is completely justified in context when you remember that he's introduced as a weak pretender taking up the mantle and armor of his mutilated idol. Keep in mind that Reploids are built for all sorts of purposes vital to maintaining their futuristic society, not just combat. He most likely was not built for physically intensive tasks or environments, thus advanced elemental defense specs ranked pretty low on the list of priorities for his internal core. So why are these weaknesses negated or neutralized in his Glint Dymonion hyper mode armor? For that matter, how can he even access a hyper mode to begin with? Simple: he's wearing the armor of the original Massimo, who was designed for intense activity. That hyper mode most likely was pre-programmed within the armor itself.
    • Zero, Axl, and Spider have noticeably lower Force Metal immunity than the other characters. Zero has a Superpowered Evil Side, while Axl's shapeshifting makes him inherently unstable, so both of them are more vulnerable to Phlebotinum Overdose. What's Spider's excuse? Being an evil shapeshifter might do it.
    • The idea that Spider somehow survived his Heroic Sacrifice explosion can be confusing to some, since it was definitely a real explosion and it looked like he disappeared in the blast - and then you remember we're talking about a guy who can turn invisible and completely invulnerable as a Hyper Mode.
    • If you speak with Gaudile during the Chapter 6-7 intermission, he'll tell you that he once offered to do some maintenance on Spider, but Spider became defensive and told him to not mess with him. Makes sense if he wanted to keep up his disguise.
    • The fact that you only fight Wild Jango, Silver Horn, Mad Nautilus (and not his inferior form Dr Psyche), Mach Jentra and Incentias in the final chapter's Boss Rush isn't just a gameplay thing but also has some basis in the story. They're the only Mavericks that could easily have their data copied unlike Epsilon and his henchmen Shadow, Scarface and Botos who are all dead, Ferham hasn't returned yet and they were Redip's main opposition, additionally Redips knew nothing about Hippopressor hence why Depth Dragoon serves the same purpose as it does. And as for Spider, well it depends on if you believe that he and Colonel Redips are the same person...
    • Another way to see the Boss Rush is that the bosses you fight had their data copied by Spider. Hippopressor isn't refought because Spider wasn't in the party at the time, Shadow was omitted because Redips was trying to maintain cover and not look suspicious and Epsilon and his rebellion are fought after Spider's death.
  • Fridge Logic: Scarface. Was he built with the scar? Did he go through life named Scarface for no good reason until his face was actually scarred? Did he change his name to Scarface after said face scarring? Is he just a really big Al Pacino fan?
    • Aile's disability, much like Overdrive Ostrich in X2. He's a robot, permanent disabilities shouldn't even be a thing for reploids (especially considering Zero and Vile had previously died and were revived without any notable issues). Was the Resistance simply lacking the resources to repair the extensive damage he suffered from?
  • Game-Breaker:
    • Axl and Spider's Stealth Modes can make the entire party all but invincible. The Bait move forces all enemies to target them, so if a Stealth Mode user performs it, the enemies will waste their moves and leave the rest of the party safe.
    • Spider's Action Trigger, if one has patience and knowledge of poker.
    • Nyanko Glove. If you feel like grinding a bit and being a haggler, you'll be able to get it in Lagrano's Secret Shop for Cinnamon early on, only for 50000 Zenny. If you don't use much money or do a little bit grinding in Infinite Forest in Gaudile's Laboratory while waiting for your Deployed Mechaniloid finding the Lagrano Key, Cinnamon would be able to wear it while she's still in Ulfat Factory. She'd be unstoppable once she wears it. 5-hits strike while wearing down enemy's ability is nifty. It is nerfed heavily in US version, though.
    • Marino's Quicksilver can be this if build right. It raises her speed to max levels, to the point that with enough Gain Hypers, the enemy will rarely get a turn and she can do as much damage as she pleases.
  • Good Bad Bugs: There's no consequence for messing up inputs during Absolute Zero's Action Trigger. This means that the player can simply mash every button on the controller to instantly perform moves, rather than waiting for commands to appear on screen, and it can lead to ridiculous amounts of damage.
  • Ho Yay: Aside from the usual X/Zero, there's also some between Zero and Spider, and Marino and Cinnamon.
  • Hilarious in Hindsight: In the climax, Zero yells "What were we fighting for?!" One cannot avoid thinking about the memetic line from Mega Man X4 which was famous for its poorly delivered voice acting.
  • It's the Same, Now It Sucks!: There are some who feel that the game's story is a typical Mega Man X story, with only added Padding to make it stand out and justify the game being an RPG instead of a platformer.
  • Low-Tier Letdown: Gameplay-wise, Massimo is the worst party member. In his basic form, he takes 150% damage from all sources, meaning despite his slightly higher than normal HP, he's incredibly vulnerable. His enhanced attack is offset by his very slow speed. His trigger into Golden Armor Massimo makes him take 50% damage from all sources, but it's limited in how much he can use it. On top of that, Massimo can only equip two Force Metals (the lowest out of the playable characters). As soon as you get anyone else, you'll probably end up pulling him out of your party and never using him again.
  • Narm:
    • This was the X series' first game with the Ocean Group doing the English dub, and you can tell they're still figuring out what directions to take the characters (their future performances in X8 and Maverick Hunter X are much cleaner).
      • X's infamous "You...you...you MAVERICK!"
      • In Cinnamon's Action Trigger, she lets out a whiny "Pleaaase~" that sounds very out of place.
      • Depth Dragoon's voice is so dorky and cheesy that it's impossible to take seriously.
    • Epsilon's Metacrush. A HP to One attack where you can only watch helplessly as someone is dragged into point-blank range of Epsilon's cannons and then sent flying... should not look like a butt-check. Alternatively, it looks as if he's farting so hard that they're sent flying by the sheer force and wind speed of his...ahem...exhaust, which also brings to mind Clone Zero's Mabu Kousou, an attack also considered narmy for the same, flatulent, reasons.
  • Narm Charm: Massimo's vengeful battlecry before the fight with Silver Horn is unintentionally hilarious, but also awesome for having a sudden Cut Short Precision F-Strike.
    Massimo: Feeble Massimo? FEEBLE Massimo!? You sunnuva-! *battle transition*
  • So Okay, It's Average: The general reaction from critics. It's no Final Fantasy or Dragon Quest, but otherwise, it's a decent RPG in its own right.
  • Spiritual Licensee: To the Breath of Fire series, also created by Capcom. This game feels more like a BoF game released for sixth-generation consoles than the actual BoF game released for a sixth-generation console.
  • Suspiciously Similar Song: The music for Hunter Base is based on a stock track; the same melody was used for the results screen in Let's Cheer! on Xbox 360 Kinect.
    • The cutscene track "Rebellion's Duty" has an electric guitar loop nearly identical to part of "Fire Away" from Devil May Cry 2.
  • That One Boss: Botos in Chapter 7 can be a real pain in the neck, hitting your party with annoying status effects and constantly summoning helpers that need to be disposed of. One chapter later, he returns as a hilariously weak mini-boss whose copy is stronger than he is, befitting his Dirty Coward personality.
  • They Wasted a Perfectly Good Character: The game falls into the trappings of many JRPGs where new party members are introduced in one chapter and then never featured again. Massimo, Marino, and Cinnamon really don't do much to affect the plot after they join the party, especially Marino who only appears in the background of one cutscene after her chapter. The final FMV of the game really nails this home - X, Zero, and Axl are shown, but the other three mysteriously disappear and are never mentioned again!
    • Marino has arguably the most intriguing backstory out of the three. From what we know, she was formerly a fashion model, and has some sort of grudge against "suits" that may have led to her Just Like Robin Hood tendencies. Despite being given these interesting plot tidbits, they never go anywhere with her character.
    • Among the bosses (Depth Dragoon, Duckbill Mole and Rafflesian) that were planned to have bigger role as chapter boss, Rafflesian is the one who got hit the hardest by the story-cutting. Not only she got demoted to a secret boss, she has no relevance to the villains and the story whatsoever other than to give the player a challenging battle to obtain X's Ultimate Armor (at the very least, Duckbill Mole is Rebellion Army's accomplice and Depth Dragoon is Redips's henchman). Her extremely petty and childish reasoning for attacking X's team certainly doesn't help things.
  • They Wasted a Perfectly Good Plot:
    • Axl can copy the abilities of certain bosses, and one of those bosses he can copy is the last of the Ninetails clan. However, instead of copying his Annihilator Hadouken, he copies the much weaker Nine Fragments attacknote  - admittedly, considering how powerful this is, it would've been a huge Game-Breakernote , but it would be sweet to use that attack - plus, by the time you can challenge said boss, you've already beaten the game anyways, so it's not like doing so would make the game too easy.
    • Similarly, while Epsilonnote  not being copyable by Axl is fair enoughnote , the fact that Ferham or Shadow can't be copied seems odd - Scarface not being copyable is somewhat justified, considering that Depth Dragoon and Wild Jango are the same element as Scarface, but no explanation exists for the other two.
    • Despite Scarface bringing it up to Epsilon, we never get to see X's Variable Weapons System in action in this game. He doesn't gain Special Weapons from defeating any bosses, and only grows stronger with EXP like the rest of the cast. They could've been an interesting addition to his arsenal, especially with the elemental alignments.
    • A lot of reviewers in more recent years have lamented that the entire game's design is this. It's touted as a role-playing game, but the reality of the matter is that only covers gearing your characters and the turn-based combat; the game itself focuses very little on character interactions and story, only having obligatory cutscenes to drive the plot forwards as several party members dip Out of Focus once their introduction arc is finished. Rather than having the whole of Giga City to explore and a world to really delve into, everything is largely glossed over and instead you just go from area to area like they wrapped the RPG formula around a linear Mega Man game. In a series with a massive pool of lore and character detail squirreled away behind platformers that can't really spare the capability to develop them, this ends up feeling like a totally wasted opportunity.
  • Too Cool to Live: Spider — or at least Redips as Spider. But depending on when Redips became him, he may even have died before the game started.
  • Viewer Name Confusion: While they might have sounded quite different to the original Japanese developers, the game's two opposing forces "Rebellion" and "Resistance" are pretty much synonymous in English. This has led to a lot of confusion, sometimes clarified by referring to Epsilon's team as the Rebellion Army to better distinguish it from X's team, the Resistance.
  • Woolseyism: In the original Japanese, Epsilon's name is actually "Ipsilon" (イプシロン). The emblem of the Rebellion Army even resembles an uppercase ypsilon (Υ), a reference lost in translation. But "Epsilon" does somehow sound cooler, so...

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