- 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.
- 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. Unlike most animal Mavericks, 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: Among the Rebellion army, a faction of extremists and anti-villains, the Reploid Silver Horn sticks out as a sadist on a perpetual power trip lacking in any of his 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.
- Ensemble Dark Horse: As far as X's numerous armor designs throughout the series go, X's redesign in this game is often considered one of the best.
- 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.
- 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.
- 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?
- Axl's Stealth Mode makes the entire party all but invincible, if you use it right.
- Spider's Action Trigger, if one has patience.
- 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.
- Most Annoying Sound: A lot of the voice acting is So Bad, It's Good, but Cinnamon's whiny "Pleeee~ase" when healing is particularly aggravating.
- X's infamous "You...you...you MAVERICK!"
- YMMV on the English voice acting, but Depth Dragoon's voice is so cheesy and odd that it's impossible to take seriously.
- Epsilon's Metacrush. A HP to 1 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 fart.
- 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 looks more like a BoF game than the actual Breath of Fire: Dragon Quarter.
- 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 pretty sweet to be able to use that attack.
- 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.
- Tier-Induced Scrappy: 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.
- 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.
YMMV / Mega Man X: Command Mission