Sigma: It's about the Maverick Hunters, General. They are far too eager to please the humans, and continue to hunt down the Reploids. Do you believe they pose a significant threat? General: Perhaps. Sigma: You already know the truth, General. Their sole mission has been to destroy any Reploids who fail to do as the humans order! General: Hm... Sigma: It's in your best interest to stop them now, before they turn on you! You possess enough power to destroy them! General: ... You are dismissed. Sigma: What?! General: I will not betray the humans. Remove yourself from my sight. My business with you has concluded... Sigma: Heheheh... very well. But you will change your mind soon, I assure you! Hahahaha... Hahahaha!
Hunter H.Q.:Mavericks have been found at point 5567! The Mavericks occupied the Sky Lagoon using the most advanced weapons available! The army appears to be the Repliforce! X: Roger that. I'm on my way now!
X: You're Dragoon from the 14th unit! Dragoon: This isn't good, X! That Maverick just destroyed the power reactor! X: What?! Then the Sky Lagoon will... come crashing into the ground! Dragoon: It's too late, X! It's time I made my escape. I suggest you do the same... Don't do anything reckless on the way out, okay? X: The city below will soon become a sea of flames. Many people will perish... I have no choice but to escape from here and head to the city below! (X travels to Sky Lagoon 2) X: ...Wha?! The city has been completely destroyed! They were innocent people... I won't forget this!
X: ...Who are you? Colonel: I'm the Colonel of the Repliforce. X: Has the Repliforce been occupying this area? Colonel: What are you talking about!? I only came to save my sister. The army responsible for all the violence in this region is not the Repliforce! X: Nevertheless, I want you to disarm and follow me back to the H.Q. Colonel: Never! You're asking my soldiers to drop their weapons? The only time we drop our weapons is when we aren't able to fight any longer! X: But you will be regarded a Maverick and treated as such. Colonel: Do as you will! The Repliforce would sooner fight and die than discard our pride! Consider us Mavericks if this is what you wish! X: Wait! Calm down Colonel! X: What the ...! Something's got to give. Otherwise the entire Repliforce will be considered to be Mavericks!
General: Brave soldiers of Repliforce, we have all been wrongfully judged as Mavericks by the humans. We cannot suffer this indignity and live in disgrace. We will build our own nation of Reploids. But remember, this is neither about insurrection, or rebellion against our human creators. This is about our liberty and security. We must battle for our own individual rights, and our own survival. Together we will build our own nation, a sanctuary for all Reploids, our own Utopia. Let us forge onward towards a new golden era for the Repliforce. Colonel: I, too, share the General's sentiment. Take heed, we have no other choice. Let us fight vehemently, with courage and pride, without fear—for we are the Repliforce. The most powerful army in history! ???: Hahahahahaha! The General has finally taken action! And now, my Maverick Hunters, what will you do? I'll be watching closely from here on out. Hahahaha!
X: ...Who are you? Double: Call me Double, the rookie Hunter. My liege, the Repliforce has begun its coup! X: ...Wait! ...Colonel, you're jumping to conclusions here! Double: Sir, you've been given the order to scramble! X: Right. I'm leaving right now!
JUNGLE: Infiltrate enemy-occupied jungle and destroy the weapon under construction.
CYBER SPACE: A bug has corrupted the network. Dive into cyberspace and exterminate it.
AIR FORCE: The Repliforce ship has taken off. Pursue and blast it out of the air.
VOLCANO: Dragoon of the 14th unit is a traitor. Locate and bring him back to Hunter H.Q.
MARINE BASE: Repliforce decimated the city and left. Pursue them aboard a Land Chaser.
BIO LAB: The abandoned lab is now operational. Investigate and destroy the lab.
MILITARY TRAIN: A military train is moving supplies. Cut off Repliforce's supply route.
SNOW BASE: We've discovered a hidden snow base. Halt production of their new weapon.
Cyber Peacock: His potential... is limitless?! ...not possible. X: Who are you? Why are you doing this to me? Cyber Peacock: I was ordered to test your abilities. It's quite simple. X: What!? Cyber Peacock: Prepare yourself!
Dragoon: X... You've arrived. X: Dragoon! Why did you betray the H.Q.!? Dragoon: Heh... You'll have to defeat me first. X: But... We're allies! Dragoon: ...You're so naive. ...Listen closely. I let the Sky Lagoon fall! And I'd do it again! Ha ha ha ha ha ha! X: No! Those were innocent people! You're not Dragoon! Just a Maverick! Dragoon: You got that right! Power up X! It's time you showed me what you can do! (X fights Magma Dragoon in a boss battle) Dragoon: ...You... are... strong... X... X: Such a waste... Why Dragoon? Dragoon: ...Always... wanted... to fight... you. ...Then ...he ...appeared ...and X: He appeared? Who?! Dragoon: Told me to work for Repliforce. To goad you into fighting... X: You did it just so you could fight me? Dragoon: ...Was worth it... for a final duel... X: Dragoon!!!
Dr. Light: This war should never have happened, X... Why must Reploids fight each other? Why do these peace keepers persist in fighting each other? This must be some sort of mistake... X, enter this capsule. Equip with this to discover the truth. Stop this tragic war as soon as possible, X.
Dr. Light: Equip with this boot module and jump twice in the air to hover. You can move either left or right and will remain airborne for a few moments. It is effective for negotiating through higher and more dangerous terrain.
Dr. Light: I'm giving you a new head module, X. This module will improve your special weapons abilities. It should reduce your special weapon energy requirements to near zero. You may now use your special weapons as often as you want.
Dr. Light: Equip with this new body module, X. This body part absorbs damage inflicted by enemies and will gradually accumulate within. When it is filled to capacity with energy you can execute the invincible Nova Strike. However, a single use will consume all your energy stores, so use it only to pull through tight situations.
Dr. Light: You can charge up to four blasts at a time with this arm module. It takes a while to charge, but you can fire a charged shot at any time you so wish with it. This arm module is also changeable. Enter this capsule to change parts.
Dr. Light: With this arm part, you can fire the Plasma Shot which is effective against stronger enemies. If the shot hits the opponent, plasma is generated which will cause additional damage to the enemy. This arm module is changeable. Enter this capsule to change parts.
Dr. Light: ...X, you've finally arrived... This capsule contains the sealed secret parts for the Ultimate Armor. When you execute the Nova Strike, the wings will open and you can execute the invincible body crash attack. ...However, this armor is not completed yet and your safety is not assured. If this is acceptable to you, enter now...
Double: Sir, it's a message from the Colonel! Colonel: X! I'll wait for you at Memorial Hall. Make sure you show up on time! Double: Sir, this must be a trap! X: ...Perhaps. But I won't run this time!
X: Colonel! Stop this foolishness now! Colonel: ...Never! X: Colonel, please! Think this over! Colonel: The Repliforce must be independent! Our battle will determine this! (X fights Colonel in a boss battle) Colonel: Impressive! But the result won't be the same next time. Until then... X: Colonel!
Double: The Repliforce has begun assembling! X: Where are they? Double: The space port! They plan to take off into space! X: Hurry! We have to stop the Colonel!!
X: Colonel, step back! Colonel: I'll stop anyone who tries to interfere with our independence! X: Enough of this! It's only an illusion! Colonel: ...You hunters will never be able to understand us! Get ready, X! (X fights Colonel in a boss battle) Colonel: ...Impressive... But... it's too late! X: What? Colonel: The Repliforce... already left for space! ...I'm beaten... but the Repliforce will never perish! ...The Reploids' nation will be born in the vastness of space! X: Colonel!!!
Double: Repliforce has flown off into space... X: ...Double, watch the ship for me. I'll go after them! Double: Sir! Reconsider what you're doing, it's far too dangerous! X: We don't have any other option! I'm leaving you in charge here, Double!
Double: Oh, not again... Hunter 1: Hey, watch it! Double: I'm terribly sorry. Sigma: It's me. Those Hunters must not be allowed in here. Terminate them! Double: Roger... Hunter 2: What a freak. All Hunters: Ha ha ha! Hunter 2: Hey, Double. What's the matter? All Hunters: Ahhh! Hunter 3: This is the Maverick Hunters, 17th Unit. Commander X, please respond! X: This is X! What happened? Report! Double: Nothing to worry about... X: No further transmissions unless necessary to carry out the operation! Double: Understood... X: I'm breaking contact. Double: And now, X will be my next target. Heh heh heh heh...
X: Double! What... Why are you here!? Double: ...Hee hee hee. Ha ha ha ha ha ha! The Mavericks, Hunters and Repliforce... Idiots, all of them. They're making my job too easy! X: ...W... What are you talking about? Double, what are you saying?! Double: Think it over in heaven! Die, X! (X fights Double in a boss battle) X: Double! Double: ...Damn! ...How could I lose to a weakling like you... X: Double, tell me! Why did you do this? Double: ...Hee hee hee. Ha ha ha! You're so naive, X! I was sent as a spy from the very beginning to keep an eye on you! X: ...Double! I... I trusted you! Double: Ha ha ha ha! That naiveness may be your fatal flaw! Good bye, X! See you in the after life! X: Double!!
X: General! What are you planning to do? General: ...We're going to build a nation for the Reploids. That's our ultimate goal. We'll fight anyone who tries to interfere with our independence. X: There must be alternatives to this mindless fighting! General: ...We were called Mavericks without justifiable reason. What other choice did we have than to fight? X: ...But... General: It's too late now! Get ready, X! (X fights General in a boss battle) X: .. what? What happened!? General: ...It can't be... This weapon must be malfunctioning... X: General! What do you mean? General: Someone else is controlling it! ...You must hurry X. The earth is... in danger! X: Alright. I'll stop the weapon myself!
???: This is amusing... It really is X... X: You're... Sigma! Sigma: Hee hee hee. My plan to keep Repliforce and the Maverick Hunters at each others' throats worked perfectly! ...Double did a good job as a spy! X: Why you...! Sigma: Hee hee hee. Repliforce are the fools this time! Now all that's left is to destroy Earth with the very weapon they made. X: No! I'll never let you do that! Sigma: Try hard X. Your life depends on it! (X fights Phantom Sigma in a boss battle) Sigma: Hee hee hee. You are very good, X! But not for long. You won't be able to evade this attack! (X fights Sigma in a boss battle) Sigma: Ha ha ha ha ha! Feel my incredible power! Drown in the empty vastness of space! (X fights Sigma in a boss battle) Sigma: ...Hee hee hee. X: What's so funny? Sigma: This weapon is aimed straight at earth already... No one can stop it now! X: Damn! Sigma: Ha ha ha ha ha! Good bye, X! X: General! General: ...The weapon can be stopped with my body. X: But then you'll... General: ...Many of my men have died. As their leader, I must leave with them... X, please forgive our foolishness... X: General!
Zero: This is Maverick Hunter Headquarters. X: Zero! Zero: It's good to see you're safe, X. I was really worried about you. X: Sorry about that. Zero: Don't worry. It's all over. Go home and rest. You've earned it. X: But Zero... What... What if I become one of the Mavericks? Zero: Don't ask such silly questions! I'm breaking contact now. X: Wait, Zero! I-I'm serious! Zero... if... if I become a Maverick, you have to take care of me. Zero: ....... Don't be ridiculous. Now hurry on back. X: ... Promise me... Zero......
...The battle has ended. Yet somehow, X doesn't feel quite right... "...What caused all those robots to turn into Mavericks? ...Will it happen to me someday?" Has X just realized his tragic destiny? It appears that X will have to solve this mystery one day... Soon...