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  • Alternate Character Interpretation:
    • Dr. Doppler's time of viral infection. Did the Sigma Virus get to him after he truly helped reform Mavericks, like it says in the intro? Or was he infected all along, and it was just a ploy to innocently gather Mavericks around himself and amass an army?
    • Dr. Doppler mentions that Vile MK-II still can't beat Dr. Doppler, even with his enhancements; this is presumably the case with Bit and Byte too. Did Dr. Doppler really make his minions weaker to prevent The Star Scream, or was Dr. Doppler secretly resisting the Sigma Virus and sabotaged his creations into making a token effort to fight X so that X would face Dr. Doppler and be the one to defeat and set him free? If X defeats Dr. Doppler's trio of dragons in the Maverick stages would this also mean Dr. Doppler has to make up to Sigma for failing him by protecting his fortress with potentially harder bosses to maintain the charade? After his Dr. Doppler's defeat, his first response is "You are strong, X... Strong enough to defeat Sigma.." suggesting he may have had something up his sleeve all along.
  • Anti-Climax Boss:
    • Considering just what a juggernaut he was to bring down in the first game, Vile is a downright pathetic boss in this game. Both of his Ride Armor fights have very predictable and limited attack patterns (basically a slightly faster Blizzard Buffalo without any real secondary attacks), and he only gets slightly trickier once he's forced to ditch the armor and go on foot.
    • Dr. Doppler only has two attacks that aren't very hard to dodge, comparable to some of the attacks of his underlings Bit and Byte but without their abilities that made dodging them much harder. While Doppler will absorb your attacks to heal when standing still, his charge attack leaves him vulnerable for a good few seconds in which the player can plug a shot into his back.
    • Kaiser Sigma makes for an incredibly difficult final boss in terms of gameplay. But in terms of being Sigma's "ultimate battle body", compared to the screen-sized Wolf Sigma and the mysterious Virus Sigma, Kaiser Sigma is just a giant robot with a fairly generic design, and it isn't even that big compared to some other Mavericks and Mechaniloids in the SNES trilogy.
  • Awesome Music: Although the soundtrack is less well-regarded than the previous two games, Doppler Stage 1 is the theme most agreed upon to be the highlight of the game. Both versions!
    • The PS1 and Saturn opening theme "One More Time" (by Shibuya Kotono) is also a nice accompaniment to the animated version of how the first two Mega Man X games went.
  • Broken Base: Some fans are divided on which version's music sounds better: the original SNES or the CD-quality version. Fans of the SNES soundtrack prefer its crunchy, almost industrial style, while fans of the CD soundtrack regard the SNES soundtrack as having too many drawn-out and repetitive notes. For some it's about the composition itself: is it as good a listen as that of the previous games, or does its more abrasive, rough-sounding tunes pale in comparison?
  • Contested Sequel: Much like the previous game in the X series, people can't seem to agree whether this game lives up to the expectations of X1. While some quality of life improvements were implemented and playing as Zero is a plus, some were either turned away by its Surprise Difficulty, the decrease in animation/graphical quality or it being too similar to the first two games.
  • Demonic Spiders: The aptly-named Wall Cancers, who if they see X or Zero charging their buster, will charge their own attack that can kill an upgrade-less X with just two hits, and even take out Zero or a fully-upgraded X with four hits. While a Gravity Well or Parasitic Bomb will easily remove them from the game, it doesn't help when their fully-charged attacks fire two deadly balls that bounce all over the surfaces, making it hard to hide from. Fortunately, they're quite fragile and a quick charge shot can destroy them before they have a chance to fire back.
  • Ensemble Dark Horse: Especially in the Japanese fandom, Mac has some ironic popularity for seeming story-important only to get curb-stomped by Zero, bordering on Memetic Loser but with a more genuine appreciation. He got a fake merch announcement in an April Fool's joke by Rockman Unity, and appeared as a character in the mobile crossover game Zombie Cafe.
  • Franchise Original Sin: While X2 was the first to officially reveal it, X3 turned the Sigma Virus into an actual plot element with its Brainwashed and Crazy effects. This unfortunately cheapened a lot of the conflicts from here on out, as many could be reduced to "he was good but now he's infected!" rather than exploring the nuances of reasons one could go Maverick on their own such as power, revenge, pride, etc.
  • Game-Breaker: Having one of the Chips makes the final levels significantly easier; having them all in the Hyper Chip (plus the Z-Saber) turns said levels into a complete joke. Mitigated somewhat by the fact that acquiring either of them makes the Maverick stages somewhat harder, with the former precluding you from getting any of the other Chips, and the latter both requiring you to face off against Vile and use Zero more sparingly, to avoid getting him killed and thereby leaving the Z-Saber inaccessible.
  • Goddamned Bats: Every single enemy, no thanks to even basic Maverick robots being able to tank loads of damage coupled with ridiculous spawning mechanics where they instantly come back as long as you so much slightly leave the screen they are found. This can lead to stupid situations where you destroy an enemy and then climb through a passage above them, only to fall down on the revived enemy due to a mistake most likely caused by a fight with a second enemy (and if you managed to kill said second enemy before falling, you'll most likely have to kill it again due to the offscreen spawning).
    • In particular, the Helit (propeller, missile-launching robot) is the worst offender. Because they spawn by coming from up above, it's possible to have multiple of them coming one after the other even if you don't leave the screen (because their spawning point is always offscreen, yet their behavior is to descend onscreen so they can attack you). They're also fairly small targets and their missiles can block your own shots, not to mention that they and their missiles need more than one hit from an uncharged X-Buster in order to be destroyed, which is always too much for what should be a simple Airborne Mook.
    • The Walk Blaster (walking cannon) is also another irritating enemy. Not only does it have a good bit of health and won't be one-shotted by a Charge Shot, it'll also crouch down to avoid most weaponry and keep firing its cannon as long as one of X's shots is onscreen, making it frustrating to hit. Finally, it's also immune to both instant-kill weapons (Gravity Well, Parasitic Bomb).
    • The Drill Wayings that drill into ceilings to create a barrier in certain stages, though not because they're a real threat. They have poor stamina and can only inflict meager collision damage if you're stupid enough to touch them, but they exist solely as an annoying pacebreaker while also being a tedious pain in the butt to kill due to the small hitboxes of their head. They're also immune to both instant-kill weapons too.
  • Harsher in Hindsight: A Dub-Induced Plot Hole states that X must destroy Zero to save mankind. At the time, this was an error, but since Mega Man X5 reveals that Sigma initiated a Colony Drop to help realize Zero's full potential, something that Mega Man X6 revealed killed most of the population, and the backstory of the Mega Man Zero series has a new AI in Zero's body kill most of the population again, this sadly becomes true.
  • Hilarious in Hindsight:
    • Dr. Doppler? You mean that dog professor guy?.
    • The turtle enemies in Toxic Seahorse's stage are called Mine Tortoise, which aren't related to mine turtles.
  • Memetic Psychopath: Bit (in the Japanese fandom at least). Iwamoto Yoshihiro, the mangaka of the Rockman X3 manga, has developed a habit of drawing Bit every Christmas, with more and more excessive Eye Pop and screaming every time.
  • Nightmare Fuel: Before the fight, Dr. Doppler threatens X by saying he's going to tear him apart and incorporate his body into Sigma's new form. They're mechanical beings so it makes sense, but it's still creepy.
  • Only the Creator Does It Right: A lot of the game development was outsourced to Minakuchi Engineering, the developers of the Game Boy Mega Man games, and it shows in the much more simplistic level designs, degree of Guide Dang It!, Fake Difficulty, and weapons that are overly-complex to the point of making it hard to use them.
  • Paranoia Fuel: After you defeat two Mavericks, Bit and Byte randomly start showing up in the sub-boss rooms in the remaining six Mavericks' levels. Not only that, but Vile lays four teleporters at the bottoms of certain pits, in some cases trapping the player into taking the teleporter and facing him in the factory.
  • Porting Disaster: The Sega Saturn version has borders on the side due to resolution problems (the Saturn hardware doesn't support the 256x224 resolution from the SNES, unlike the PlayStation, which forces the game to run at 320x240 with colored bordes filling the empty space) making the characters look more skinnier, longer loading times and more slowdown. The only advantage over the PlayStation verison is the higher quality FMV's.
  • Polished Port: The PlayStation and PC versions of X3 has enhanced CD-quality music, new animated cut-scenes, and a save feature. The downside of these ports was the loading times, which was eradicated in its inclusion in the X Collection, while the PC version's load times are significantly reduced when played on higher-end systems. YMMV on this, however, because many people were unhappy that it wasn't the SNES version that would later be featured on the Wii U Virtual Console release and the X Legacy Collection.
  • Popular with Furries: Although a good many Reploids are designed after cool animals, Neon Tiger emerged as a Furry favorite because of his striking design and Wolverine Claws made of plasma. Of note, he is the only Mega Man character to have an article on WikiFur.
  • Scrappy Mechanic:
    • The Arm Parts may look flashy, but the fact that it briefly stops X in his tracks and has a slight delay on its fully charged blast can be a source of annoyance if you're trying to attack enemies quickly. The main reason to get the upgrade at all is to enable the Hyper Chip and Z-Saber. One well-known speed runner, Hide of Beast, has gone on record calling it "emasculating".
    • The Head Parts is also a source of annoyance, forcing you to watch a map of the area each and every time you enter one of the main Maverick levels, even if you've already found everything there is to find. And if you want to open the map again while in the stage, you can't; it only gets shown upon entering the stage.
    • Fans who work their way backward from a later Mega Man X game will be disappointed to find that Zero cannot fight regular bosses and will be permanently unusable if he dies (though the last bit is more understandable if the unlock conditions for his Z-Saber are met).
    • The upgrade Chips for X's Third Armor. The four standard Chips are each hidden in one of the stages, like the armor parts are. You'd think you can collect them all, just like the Parts, making you even more powerful, right? Nope. Grabbing one means you can't get the other three. Worse, getting any of them means you can't find the secret capsule in Doppler Stage A (already an example of Guide Dang It! thanks to its hidden location), which grants you the Hyper Chip, giving you the effects of all four Chips and coloring X's armor gold. Why didn't they just let you collect the four Chips as would be expected and color X's armor gold as a sign that you collected them all?
  • So Okay, It's Average: While some argue X3 is a weaker entry in the X series, it's also regarded as a decent game overall. Despite bringing new innovations to the series (most notably the Chips, multiple Ride Armors, and alternate routes), it falls flat in terms of collectibles which involves a lot of backtracking, similarly to that of Mega Man X5, not to mention bosses that are easy to trap in predictable patterns.
  • Suspiciously Similar Song:
    • Crush Crawfish's theme sounds similar to the original Mighty Morphin' Power Rangers theme.
    • A little infamously, Neon Tiger's theme (especially on SNES) resembles the Guns N' Roses song "My Michelle" (the composer Kinuyo Yamashita was asked about this one in an interview, and said it was a coincidence).
    • Volt Catfish's theme sounds like another Guns N' Roses song, "It's So Easy".note 
    • The music for the opening stage sounds a lot like "Distopia" by Megadeth, a song that would be released several years after this game came out. It's possible Megadeth got the idea for Distopia from this game.
    • The CD version's overseas opening theme (replacing "One More Time") has a guitar line that sounds an awful lot like the one in "Beat It" by Michael Jackson, and also resembles the main theme of Killer Instinct near the beginning.
  • That One Attack: Fighting Volt Catfish without his weakness wouldn't be so bad if not for the attack he gains when he Turns Red. For this attack, he will stand in the center of the room, create two breakable shields on either side and fill the top of the room with randomized sparks before charging at the player after a set amount of time. If the player manages to jump over Volt catfish's charge attack (and they will probably have to break the shield on their side to reduce his width), there is a chance they might get hit by one of the randomized sparks during their jump. Tornado Fang trivializes this attack by immediately breaking through Volt Catfish's shield and stunning him, but if you don't have it, good luck breaking his shield and taking a leap of faith!
  • That One Boss: Even by Final Boss standards, Kaiser Sigma is brutally difficult thanks to the fact that the only place to damage him is his tiny head that's deceptively difficult to actually hit (unless you know that you actually be aiming for his shoulder pads instead, because trying to shoot his head directly will almost certainly get your projectile blocked by his shoulder-mounted laser.) He can only be hurt by fully charged shots in a game where the Buster upgrade makes things harder or the Z-Saber that will be canceled out if you are hit before slashing him. What's worse, if one fails the ensuing climb after Kaiser Sigma's defeat, they'll have to do it all over again.
  • That One Level: The Doppler stages.
    • Stage 1 starts with a series of low-hanging spike ceilings suspended over pits. If that weren't enough, there are enemies waiting for you that could potentially make you fall, and they're too far away for you to shoot from the other end of the pit. Once you're done with that irritation, you then have to quickly scale closing-in walls.
    • Stage 2 for the most part is manageable until you reach the infamous Snail Wall. You're surrounded by spikes, and the only way to bypass them are a few snail enemies that you shoot to make a platform. They move slower than molasses, and you have to be careful not to over-jump to the next snail, lest you get killed by the spikes. To make matters more annoying, one snail is a small section of spikes, tricking the player to jump off. One false move, and the player has to go through that tedium all over again.
  • They Changed It, Now It Sucks!: The complaints of the disc versions of X3 amount to this, as the main difference is the arranged soundtrack and sound effects. This was enforced when the Mega Man X Collection included only the arranged version, and was the easiest-accessed version for years. Thankfully, the Mega Man X Legacy Collection included the original SNES version of X3 instead of the arranged version, creating a balance.
  • They Wasted a Perfectly Good Character:
    • X not only has Bit and Byte pursuing him, but also a Doppler-resurrected Vile acting on his own. Since the three Co-Dragons have to share the spotlight, they end up both overcrowding the game while also seeming too shallow to merit inclusion at all. And then there's the question of what Bit, Byte, and Vile all think of each other - it's borderline Fanfic Fuel. The manga tries to rectify this by making Bit and Byte the only servants of Dr. Doppler, acting as Disc-One Final Bosses of sorts until Vile appears alongside Sigma for the true climax.
    • Mac was clearly meant to be a flat character made to let the players try out Zero. But the idea of a traitorous Hunter whom X once trusted is an interesting concept that could have been explored more (see Double in X4).
  • They Wasted a Perfectly Good Plot: Having Doppler's troupe as a brand new villainous force could have allowed for a new perspective into what makes a Reploid go Maverick. This opportunity is overpowered by the reveal that the Sigma Virus is involved and can literally just force Reploids to go Maverick. Subtlety is out the window at this point, though future games such as X4 and X8 attempt to bring the grey morality back.
  • Woolseyism: The name change for Bit and Byte, which changed them from an obscure mythological reference into something memorable, if not a bit goofy.
  • Unfortunate Character Design: The Hell Crusher miniboss from Tunnel Rhino's stage has a giant spike located in a rather questionable part of his body.
  • Underused Game Mechanic:
    • This is where the Ride Armor system is taken the furthest in the series, yet the only true utility of the various armors is in finding other hidden upgrades.
    • Zero is playable for the first time, but can't fight most bosses (except for a certain Mini-Boss), and cannot be used again if he dies.

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