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1* AntiClimaxBoss: The final boss, Sigma, is significantly easier than the rest of the game. His first form is a complete joke, almost to the point of being a ZeroEffortBoss even if you don't use his weakness, as he just lumbers around the room and fires off attacks which barely even scratch you. His second form is somewhat more challenging, as his attacks can do serious damage if they connect, but he follows a predictable pattern and there are several safe spots in the room, meaning it's still quite manageable; [[FlunkyBoss the green blob-heads that he spawns]] can sometimes drop life energy (and even 1-ups!) if they're destroyed. Zero especially will have a good time attacking him with Guard Shell-enhanced normal saber attacks or Ensuizan.
2* AssPull:
3** Zero's infamous UnexplainedRecovery. X wonders how he survived, causing Zero to state the infamous "[[BlindIdiotTranslation I hid myself while I tried to repair myself]]" line. Keep in mind that ''VideoGame/MegaManX5'' was supposed to be the last ''X'' entry, ending with his death. Furthermore, his next appearance was going to be his reemergence ''centuries'' later as seen in ''VideoGame/MegaManZero1'', making it clear that the dev team just {{Handwave}}d him into ''X6'' with no real thought whatsoever. While players never get a coherent explanation beyond what Zero tells X, an exchange between Zero and [[VirtualGhost Dr. Light]] has Zero admit he really doesn't know who was responsible for his repairs while in a critical state. Dialogue from [[MadScientist Isoc]] instead suggests ''he'' was largely responsible for Zero's restoration between games -- which might be a hard pill to swallow given [[BlackBox Zero's nature]] if not for the fact that, like Serges before him in ''VideoGame/MegaManX2'', Isoc is implied to be [[BackFromTheDead an incarnation of Dr. Wily]] (who was established to be Sigma's benefactor in the previous game by WordOfGod).
4** [[HijackedByGanon Sigma being revived]], seeing that ''he wasn't even mentioned once in the game until that point''. (Not counting the intro, of course.) The only reasons players were expecting it at all or not surprised by his sudden appearance were a) it's series tradition for [[JokerImmunity Sigma not to stay dead]] and b) Gate's plans involved the use of Zero's viral DNA, which was the original form of the Sigma Virus.
5* SugarWiki/AwesomeArt: One thing the fanbase ''does'' agree on is that the sprite work looks awesome, some even considering it some of the best in the series.
6* SugarWiki/AwesomeMusic: Players often describe the music in this game as some of the best in the franchise ([[AwesomeMusic/MegaManX which is no easy feat]]), and even detractors usually have no problem admitting as much, leading many to wonder if Creator/{{Capcom}} put more time and effort into the songs than the actual game. Standout examples include (but certainly are not limited to):
7** [[https://www.youtube.com/watch?v=bn5LFvpSjlM The intro stage's theme]] starts the game's soundtrack off on the right foot: a somber, but cathartic piece, which perfectly describes the calamity of the crash site ruins. [[https://www.youtube.com/watch?v=CoXmFmRurBI The international version]] adds in a couple of guitar riffs here and there, which gives the song a lot of flavor and shifts the mood to something a bit more hopeful and action-y.
8** Blaze Heatnix's theme is a fast-paced guitar track that never lets up, and is so rocking that it's common to see people complimenting the song and [[ThatOneLevel hating the level]].
9%% Individual examples listed above may need to be moved to the corresponding page: AwesomeMusic/MegaManX
10* BigLippedAlligatorMoment:
11** After the boss of the intro stage, the D-1000, is defeated, it isn't completely obliterated after it explodes. Suddenly, the [[EvilKnockoff Zero Nightmare]] teleports in, slashes the D-1000's remains, and then teleports away as the latter explodes again. This time, there is no trace left of the D-1000. It comes across as a poor attempt at allowing X to be aware that Zero may still be alive...for some reason. Furthermore, it's never explained why the Zero Nightmare helped X in the first place, with later encounters only establishing it has [[MoodSwinger a very erratic personality]] and possibly some of Zero's memories yet never following up from that first appearance -- despite the fact that the Zero Nightmare sometimes attempts to pass itself off as Zero.
12** Dynamo. To fill up the Nightmare boss rooms once the Zero Nightmare and High Max are beaten, he's chilling there and collecting Nightmare Souls. That's all there is to his relevance.
13* BreatherBoss:
14** Ground Scaravich is by far pretty easy, and is almost an apology for how infuriating his randomly generated level is.
15** The relative ease of Blaze Heatnix's battle could be an apology for how annoying the [[GoddamnedBoss Nightmare Snakes]] miniboss gauntlet in his stage is.
16** Just like he was in ''X5'', Dynamo (one of the {{Optional Boss}}es) is the easiest boss in the game, compared to the Nightmare area you have to traverse to get to him. He also falls down easily to his weakness weapons, and if you do so, he drops a big Nightmare Soul (which you normally get from the eight bosses, for 200 points), up to three times. And the best part? You can engage him countless times.
17* BreatherLevel:
18** Shield Sheldon is mercifully brief, and much more forgiving in difficulty than the rest of the game.
19** Infinity Mijinion as well, as it's the second shortest main level of the game (after Sheldon's) and has the easiest access to its Nightmare portal; its Nightmare area is also short, allowing you to reach its boss room (and [[PeninsulaOfPowerLeveling Dynamo]]) easily.
20* BrokenBase:
21** Some players enjoy the difficulty and stage designs and others absolutely despise them, with little to no middle ground. It is undeniably a different kind of challenge than what Mega Man players are used to.
22** Zero has a completely different sword combo in this game from ''[[VideoGame/MegaManX4 X4]]'' and ''[[VideoGame/MegaManX5 X5]]'' (done to [[{{Nerf}} put a kibosh on]] his [[GameBreaker game-breaking]] [[LagCancel slash-dash cancels]]), and whether players appreciate the change largely boils down to whether they enjoy the rest of the game or not.
23** Depending on who you ask, the presence of Japanese voices are either a proof of how poorly executed the game was or a good thing considering the bad quality of the English dubs in ''VideoGame/MegaManX4'' and ''VideoGame/MegaManX7''.
24* CatharsisFactor: There's a big feeling of satisfaction to be had after successfully rescuing all 128 Reploids without losing one.
25* ComplacentGamingSyndrome: Difficult or not, players often go to Mijinion's level first since that's where the [[BrutalBonusLevel Nightmare area]] is reached both the fastest and easiest, so as to unlock Zero as a playable character. Speedruns especially go with defeating just Sheldon for his Guard Shell, and then go defeat High Max in one of the Nightmare stages to unlock the Gate's Lab stages early.
26* CriticalBacklash: ''Mega Man X6'' received mediocre reviews from critics (scoring 65 at Metacritic) and has been torn apart by a great part of the fandom as one of the weakest installments in [[VideoGame/MegaManX the series]], but some fans like to give it some credit. They appreciate the harsh difficulty of this game as a fun challenge (as ''VideoGame/MegaManX4'', while far more popular, [[ItsEasySoItSucks draws some criticism for being too easy]]), the gameplay upgrades over the previous Platform/PlayStation ''VideoGame/MegaManX'' games (''X4'' and ''[[VideoGame/MegaManX5 X5]]''), the more balanced focus between X and Zero, and giving Alia more relevance to her character. Despite its confusing nature and its overdone difficulty (both of the {{fake|Difficulty}} and [[NintendoHard legitimate]] varieties), the difficulty actually is a selling point for some.
27* CriticProof: Despite reciving middling to negative reviews due to its rushed quality and Main/FakeDifficulty, it managed to sold 100k copies by the end of year in Japan, which by a game released at the end of November was quite impressive, and saw a re-print under the "[=PlayStation=] the Best" label the next year.
28* FanNickname: The Nightmare Snakes in Blaze Heatnix's stage are often called "Donuts" due to [[{{Ouroboros}} their motif]] combined with their visually confusing sprite causing them to look as such.
29* FauxSymbolism: For some reason, Gate's heavily fortified lab entrance has figures/statues that resemble a semi-mechanical devil and a similarly semi-mechanical headless angel. As you progress through the stage, the devil statue gains bat wings, and finally stands as if roaring, while the angel statue gets chained and progressively stripped of materials. Probably a vague commentary on Gate's SanitySlippage, but it ends up comes off as tacky since religious themes barely have anything to do with the series except for ''[[VideoGame/MegaManX8 X8]]''.
30* EventObscuringCamera: Most egregiously in Commander Yammark's Amazon Area, forcing the player into a LeapOfFaith onto spikes and a caterpillar platform. It's ''very'' easy to miss the caterpillar and die instantly.
31* GoddamnedBats:
32** Aside from infecting civilian Reploids so you can't rescue them, Nightmare Viruses can pass through walls (in a game where your shots can't), have an aggravating projectile attack and lunge attack, and take a ton of hits to kill. And even if you kill them, if you don't grab the Nightmare Soul that's left behind in a timely manner, they'll quickly respawn.
33** Nightmare bugs that surround X/Zero. They're an InvincibleMinorMinion (unless you use Yammar Option), and harmless...except they will literally get in the way of X/Zero's attacks.
34* GoddamnedBoss:
35** The Nightmare Snakes of Blaze Heatnix's stage. They're not that difficult to deal with, but they have [[DamageSpongeBoss ridiculous HP]] and spread shots that are deceptively hard to dodge. Oh, and there's '''[[BossBonanza five]]''' of them, which you have to engage sequentially. If you don't have the right tools to finish the battles faster, then it becomes a total chore as you pathetically run around those things, shooting/slashing each of the four glowing weakpoints every Snake carries. The fourth one in particular is TheDreaded for being fought during a [[RiseToTheChallenge climbing sequence]] where half of the screen consists of fire and the other a random assortment of platforms and Nightmares that only serve to get on your way.
36** High Max's new pattern in the Secret Lab. It's not that you can't hurt him by that point in the game; but it can take some time to get a shot in on him [[note]]unless you use Blade Armor's ChargedAttack[[/note]] that you'll be waiting for a long ass time to get that hit in.
37* GoodBadBugs: Due to the game's rushed development, there are plenty of ways to break it. Unsurprisingly, Zero hoards the lion's share.
38** The Guard Shell wreaks havoc on any enemy's MercyInvincibility, letting you deal tons of hits at once. It's especially nasty with Zero's standard jump attack: activate it, get close enough, and you can jump-slash bosses to shreds in ''seconds''. It's even faster than ''X4'' and ''X5'''s infamous [[LagCancel slash-dash-cancel]] (which is still possible in this game, but is made obsolete by Guard Shell's insane power).
39*** X can also use the Guard Shell bug with the Blade Armor's Mach Dash, which is one of the fastest ways to take out High Max: activate it, stun him with a Charge Shot, then hit him with a Mach Dash to deal more damage at once than ever normally possible.
40** Ensuizan messes with Zero's invincibility; the game makes him invincible when starting Ensuizan and only removes it as the spin ends. If Ensuizan is interrupted somehow (such as destroying the platform Zero's standing on), Zero can keep the invincibility for the rest of the area since the spin technically never ended. Entering a new area or using another Ensuizan cancels the effect.
41** X's Magma Blade resets his gravity. He can glide against otherwise uncrossable BottomlessPits by spamming the blade while in midair.
42* HilariousInHindsight: Turtonator from ''VideoGame/PokemonSunAndMoon'' has the exact same stance as Rainy Turtloid, which people familiar with ''X6'' made out immediately upon its reveal.
43* ItsHardSoItSucks: The game's ''very'' high difficulty (both {{fake|Difficulty}} and [[NintendoHard legitimate]]) is known to alienate more than a few players, although others are actually attracted to the game because of it.
44* ItsTheSameNowItSucks: For all of the changes later releases of the game have made, fixing the infamous BlindIdiotTranslation is not one of them. There's also been some requests to re-map Sentsuizan's command to Down+Attack instead of Up+Attack due to the frustrating rope segments, but this was never changed either.
45* ItWasHisSled: That Zero is alive, which is important because Zero was explicitly destroyed in the previous game. Then again, with [[SpoiledByTheManual the manual]] mentioning a "Resurrected Hunter" '''who cannot be anyone other than Zero''' as a SecretCharacter, featuring artwork of X and Zero [[BackToBackBadasses back-to-back]] (with X looking pretty chipper for a guy whose best friend is supposedly dead), ''and'' stating that [[{{Retcon}} Zero is merely MIA as opposed to KIA]] (along with the back of the game case reading "Zero is Missing"), one wonders if Capcom actually intended for this to be a secret at all.
46* MorePopularReplacement: Some fans believe that Gate served as a better BigBad than Sigma did, citing that his involvement in the story is more personalized, that he has a unique backstory and dynamic with Alia, and that his ultimate plan of a MonsterProtectionRacket to let society know of his genius when they had previously turned it down is [[TheChessmaster brilliant]]. It also helps that, unlike [[VideoGame/MegaManX3 Dr. Doppler]], [[VideoGame/MegaManX4 Repliforce]], or [[VideoGame/MegaManX7 Red Alert]], he's not actually [[HijackedByGanon being used by Sigma]], and is instead using Sigma as ''his'' [[GodzillaThreshold secret weapon]], which is a concept that ([[AmbiguousSituation depending on who you ask]]) wouldn't be explored again until Lumine in ''[[VideoGame/MegaManX8 X8]]''.
47* SugarWiki/MostWonderfulSound: [[https://www.youtube.com/watch?v=-arH4cwIsLM Zero's victory theme]], especially after an extremely difficult level.
48* {{Narm}}: After you defeat Gate, he reveals that he resurrected Sigma as a last resort. Sigma claims he didn't need Gate to bring him back from the dead and brutally injures him, and Gate lets out a ridiculously high-pitched and drawn-out scream which sounds way more hilarious than it should have been given the circumstances.
49* ObviousBeta: This game was rushed out in ten months, and it shows in many places.
50** Many enemy sprites and music tracks are recycled from previous games. (Curiously, the latter tracks are missing from the sound test.)
51** The level design ranges from barren to sloppy and uneven, and most of its challenge comes from FakeDifficulty tricks.
52** The game is seemingly designed around the Falcon Armor, its upgrades, and Zero, and is near-impossible to play as unarmored X. Several Parts are even harder or legitimately {{Unwinnable}} without specific Parts or armors; most Parts are [[PermanentlyMissableContent lost forever]] if you can't rescue their respective Reploids. And the game [[GuideDangIt never tells you to find them beforehand]].
53** As listed in GoodBadBugs, there are glitches that can absolutely break the game's difficulty, such as using Magma Blade to fly or doing a simple trick with Zero to become completely invincible to everything except being crushed. He's even immune to spikes in this state.
54** Zero's special upgrade, Black Zero, is only obtainable through an in-game code on the title screen. However, it was intended to be possible to obtain it in normal gameplay, by beating the Zero Nightmare when it is at Level 4, requiring you to collect 5,000 Nightmare Souls. The issue comes from the fact that you unlock the final stages with 3,000 souls due to an oversight, and once you unlock those stages [[PermanentlyMissableContent you cannot fight it at all]], making the Black Zero armor impossible to obtain without the code.
55** The localization was so rushed that the English script became a BlindIdiotTranslation full of terrible grammar and nonsensical lines, and the Japanese voiceovers were left intact.
56* PolishedPort: The ''Legacy Collection'' version has the Rookie Hunter mode, which cuts the difficulty to more bearable levels.
57* PortingDisaster:
58** The Korean-only PC port has much higher system requirements than the ports of ''X4'' and ''X5'' and has noticeable screen flickering problems.
59** To a lesser extent, the version of ''X6'' found in the ''[[CompilationRerelease X Collection]]'' removes most of the voices, mainly to minimize the Japanese. Fans were not pleased.
60* RescuedFromTheScrappyHeap: This game took the first steps on upgrading Alia by making most of her calls skippable, more relevant, and less of a shoehorned tutorial. She also got an intriguing backstory featuring Gate too.
61* TheScrappy: You are ''not'' going to enjoy fighting [[MesACrowd Infinity Mijinion]]. Not only is he ThatOneBoss, but he has annoyingly high-pitched voice lines and sound effects to boot.
62* ScrappyMechanic:
63** Rescuing Reploids. The devs sought to better develop the system as the players believed it to be underdeveloped in ''X5''. However, their mortality from Nightmare Virus possession ruins the fun this could have had. This is worsened by the fact that some carry with them Parts that may be necessary for you to complete certain objectives, and when they die (due to the Nightmare Virus infecting them -- and they may be put ''very close'' to those Reploids), so do your chances of obtaining them. It becomes so distracting to the overall gameplay experience that a few people view it as an irritation rather than a feature.
64** The Nightmare Phenomenon. Although comparable to ''[[VideoGame/MegaManX1 X1]]'''s own stage effects, they are far more detrimental here. Special mention goes to Infinity Mijinion's [[BlackoutBasement Nightmare Dark]], which renders Commander Yammark and Rainy Turtloid's stages near-unplayable. Another is the Yammark Nightmare which produces little flies that take some immense punishment to get rid of unless you shoot them with with the Yammar Option. Zero has no trouble with them, but they love to get in the way of X's shots. What's more, the game is [[GuideDangIt vague on what exactly triggers a Phenomenon]] in the first place and more importantly how to get rid of it. [[note]]Each stage has two specific Phenomenon that can affect it at a time, and going to a stage will trigger its related Phenomenon in the other affected stages. However, each stage can only have one active Phenomenon at a time. The only way to get rid of the Phenomenon in a stage is to play ''another'' stage to trigger the other specific Phenomenon. Good luck memorizing which stages are affected by which Phenomenon triggered by what source stages, on top of either completing the stage in question or just killing yourself several times to force a game over and return to the stage select screen manually to get the desired Phenomenon.[[/note]]
65** The secret areas are very tough. They are reached through blue teleporters (which are also sometimes used to just get to the next part of the stage) and you're trapped once you go inside, forcing you to face whoever's waiting in the boss room before you can exit. If it's the Zero Nightmare, it's not that big of a deal, but if it's High Max and you're unprepared...either try to defeat him before you're ready, or kill yourself until you can return to the stage select screen. (And thanks to the Reploids all giving you extra lives, this may take a while too.)
66** As part of the {{nerf}} to Zero's [[GameBreaker game-breaking]] LagCancel antics in the previous two games, the Z-Saber is now rather slow in its slashes. This is problematic when Zero goes against invulnerable targets, since the final slash can last very long and cannot be canceled.
67** As previously mentioned, getting Parts is a Scrappy Mechanic in and of itself; getting the ability to '''equip''' a lot of them stinks. You have to collect a ton of Nightmare Souls to boost your Rank, which is tied to your ability to hold Parts. To be able to equip three or four Parts, you have to collect over 5,000 and the maximum 9,999 souls respectively. The souls however only go eight per Nightmare Virus (four if you let the orb shrink from not grabbing it fast enough), 200 for each of the eight Nightmare Investigators (and if you take too long to defeat one, you'll actually only get ''100''), and 600 per [[OptionalBoss Dynamo]] encounter if you hit him with his weakness weapon and make him drop three souls worth 200 apiece. The grind is so tedious and frustrating that many just settle for two Parts and a Limited upgrade (which only requires 1,200 souls, which is bearable in a normal run for both X and Zero without much grinding).
68* ScrappyWeapon:
69** The Guard Shell is meant to protect from and reflect enemy shots, but the attacks of several enemies (including Nightmare Viruses, the most common enemy in the game) will simply pass through the shield. If the shot ''is'' compatible with the shield, it won't be reflected right away and take a moment to charge up in which the enemy can just move out of the way. Also, it is supposed to be Infinity Mijinion's weakness, but it barely does any damage to him and forces the player to rely on the boss doing specific moves to even work at all. Because of this, many consider the Yammark Option to be a better "weakness" to Mijinion than the actual weakness. However, it has a decent charged version and as noted in GoodBadBugs above, Guard Shell somehow empowers Zero.
70** Sentsuizan has its detractors for making rope sections even harder. If you keep Up pressed down and need to do a saber attack, Zero will instead dive to the floor or, much worse, spikes or BottomlessPits. This is most apparent in the secret area of Infinity Mijinion's stage, the Weapon Center, which has almost no solid footing and relies mainly on rope navigation.
71* SeasonalRot: ''Mega Man X6'' is usually considered the weakest of the [=PlayStation=] games, and one of the least popular games in the ''Mega Man X'' series overall. The low points include the poor localization, being extremely difficult [[FakeDifficulty for all of the wrong reasons]], [[FranchiseZombie being an unplanned sequel]] that caused more confusion plot-wise, and the rushed development cycle [[ObviousBeta clearly showing in the final product]].
72* SequelDifficultySpike: Generally considered the hardest game in the ''X'' series and one of the hardest in the whole ''Mega Man'' franchise.
73* SpoiledByTheFormat: Fans used to the series traditions might have been able to tell that there's more after Gate because of how the BossRush hadn't happened yet.
74* SuspiciouslySimilarSong: Inifinity Mijinion's theme starts with a synth brass riff that sounds just like Music/{{Europe}}'s "The Final Countdown", Metal Shark Player's theme bears a resemblance to the main theme of ''Film/TheTerminator'', and Gate's Secret Lab theme is a reprise of the second X-Hunter Stage theme from ''VideoGame/MegaManX2''.
75* ThatOneAttack: Gate's orb attacks. To damage Gate at all, the player has to blow the orbs up and let the backlash from each orb hit him. However, you're constantly above a bottomless pit during the entire fight and the orbs that launch back at him also shoot at the player who is likely too close to the orbs to get away without taking a hit. You can straight up lose the fight if you don't have two full Sub Tanks with you into the battle.
76* ThatOneBoss: [[ThatOneBoss/MegaMan Has a page.]]
77* ThatOneLevel: [[ThatOneLevel/MegaMan Also has a page.]]
78* TheyChangedItNowItSucks:
79** The [[{{Nerf}} downgrades]] to the Falcon Armor (e.g. removing its nigh-invincible flight in place of an {{air dash|ing}}, charge shots can't go though walls anymore) were understandable given how much of a GameBreaker it was in ''X5'', but the strip-down was so bad -- especially in the face of [[SequelDifficultySpike the game's upscale in difficulty]] -- that it was poorly received by players.
80** The ''X Legacy Collection 2'' release completely replaced the original opening and ending songs with new tunes that many fans didn't find as memorable or fitting. Even worse, even switching to the Japanese version doesn't help with this. This doesn't apply to the Japanese release of the collection, however, since all songs were kept there (suggesting [[ScrewedByTheLawyers licensing issues]] may have played a hand).
81* TheyWastedAPerfectlyGoodCharacter:
82** There a few hints that imply that Isoc is actually [[BackFromTheDead a vessel for Dr. Wily]] (hints include calling Zero a "robot" instead of a Reploid as well as [[VillainTakesAnInterest having a vested interest in Zero]] while showing X nothing but contempt), but he "dies" at the end and nothing comes out of this. The only assumption is that it was a plot point to be followed up in a sequel, but ''X7'' and ''X8'' [[AbortedArc never even come close to bringing up Isoc again]]. Also, despite being shown to be able to paralyze Zero (and therefore that he has some extra powers at his disposal, or at least the ability to tamper with Zero given his knowledge of Zero's inner workings), he is one of the only villains in the series to be TheUnfought.
83** Like [[VideoGame/MegaManX3 Dr. Doppler]] before him, Gate was ''almost'' the series' first antagonist to not have anything to do with Sigma. His [[TallPoppySyndrome interesting backstory]] and [[FoeRomanceSubtext relationship with Alia]] were more than enough to make him a potentially compelling villain. And what did they reveal in the end? Well...
84** Sigma is [[GiantSpaceFleaFromNowhere so superfluous to the plot]] that he might as well have been left out. The idea of a desperate Sigma on his last legs is explored much better in ''X8'', where his vulnerability pushes him to FlingALightIntoTheFuture for his Maverick dream, rather than just being [[RoboticUndead an angry zombie]]. It doesn't help that Sigma was meant to stay dead after ''X5''.
85** After [[WhatHappenedToTheMouse disappearing from]] ''X5'' as a KarmaHoudini, Dynamo is back, and is mirroring the player by collecting Nightmare Souls. Unfortunately, instead of being a plot-relevant rival gradually powering himself up over multiple encounters using his collected Nightmare Souls the same way the player does, he's a [[LoneWolfBoss completely irrelevant]] OptionalBoss with only one variant, you still can't give him his comeuppance, and [[ChuckCunninghamSyndrome he hasn't made an appearance since]].
86* TheyWastedAPerfectlyGoodPlot:
87** As it is completely possible to beat the game without unlocking Zero, the game could have taken the opportunity to explore X having to fight on his own for the first time in a while by changing his cutscenes depending on if Zero has reunited with X or not to show contrast between how he handles conflicts under his current circumstances. Instead, the only X-exclusive cutscene to be adjusted by Zero's presence (or lack thereof) is the final one, and since every other scene has to work with or without Zero, there isn't a chance to develop the impact of X fighting by himself.
88** Sigma was meant to be permanently defeated at the end of ''X5''. ''X6'' brings in new villains like Gate (a Reploid researcher with ties to Alia who was ostracized for his intelligence) and Isoc (Dr. Wily's implied vessel), suggesting the game would take a slightly different path from previous entries but continue to build upon certain aspects of the ''X'' series' MythArc. Instead, Sigma becomes the FinalBoss as usual (even claiming in a rare moment of clarity that he didn't even need Gate's help to return) and Isoc disappears from the plot altogether in its closing stages, meaning StatusQuoIsGod and the bombshell reveal that [[GreaterScopeVillain Wily]] [[JokerImmunity is still around]] and [[TheManBehindTheMan directly influencing events]] [[AbortedArc goes nowhere]].
89** Isoc's presence and the implications of his character, while solving the issue of Zero's UnexplainedRecovery, [[VoodooShark raises a few other questions as a result]]. The biggest is Isoc going through the trouble of repairing Zero ''without'' trying to "fix" his programming -- which was the goal of Sigma and Wily's EvilPlan in the previous game (and canonically failed to happen). This also could've been a way to give the Zero Nightmare more relevance to the plot, as while he's an EvilKnockoff created by Gate as [[FalseFlagOperation a means to justify the existence of the Nightmare Investigators]], he appears to have some of the original's memories. (Note how X's exchange with him in the secret area of Blizzard Wolfang's stage has the Zero Nightmare refer to X as a blue '''robot''', for example.) [[Administrivia/TropesAreTools On the other hand]], fans would've likely seen anything regarding [[FaceHeelTurn a Heel-turned Zero]] as [[RecycledScript a rehash]] of both the aforementioned ''X5'' and the Fake Zero scenario from ''X2'' (which coincidentally featured Serges, another character implied to be an incarnation of Wily). Additionally, while out-of-canon, ''VideoGame/TatsunokoVsCapcom'' shows Wily delivering Zero to safety after the FinalBoss and [[SoProudOfYou expressing pride in Zero's accomplishments]] despite the fact that [[AntiAntiChrist he never fulfilled his original purpose]], possibly explaining away Isoc's decision to let Zero be and sing his praises should he triumph over High Max.
90* ViewerGenderConfusion: Commander Yammark can be confused for a woman at first glance, what with those big eyelashes and slender frame... Then you get into battle and hear his surprisingly masculine voice.
91* TheWoobie: Several villains in this game alternate between this and JerkassWoobie (with the exception of Blaze Heatnix because he's ''just'' [[{{Jerkass}} an asshole]]). Put simply, several of them are victims of unfortunate circumstances that ended with being unjustly labeled Mavericks, or in Gate's case, [[PersecutedIntellectuals the victim of]] [[AllOfTheOtherReindeer being looked down on]] [[TallPoppySyndrome for his creations being too powerful]], despite the existence of X and Zero being accepted.

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