For some unknown reason, the programs of Reploids are suddenly erased. The Reploids stopped moving and almost seemed like they had become hollow shells. This phenomenon was named "Erasure" and began to frighten the Reploids....
"Laguz Island" in the Southern Ocean here is where the Reploid Research Lavatory is located. One day, the readings of Reploids had instantly vanished. A lot of Reploids were erased! What happened in this island.....? Maverick Hunters, X and Zero received the orders and head into action!

Iris: You are now on Laguz Island where the Erasure Incidents have happened. What's the situation there?
X: I have found some Reploids that are out of commission, and the others have become Mavericks.
Zero: Iris, we will begin to check the surrounding area. Can you offer us support?
Iris: Okay, but please don't get too wild and bite off more than you can chew.
Zero: Don't worry, Iris.

X Mission:
Zero: Did you find anything, X?
X: Yes I found something! The island is filled with the Mavericks that I thought we had destroyed.
Zero: What?! Did they come back by themselves, or is there someone behind their resurrection? We must find out.
X: I'll go and check it out.
Zero: Okay. Let's meet up again later.

X: What's this place? Hm! The enemy is coming!

X: Are you alright, Zero?
Zero: There seems to be so many more enemies.
X: This is crazy! What is their purpose, anyway? I must find out!

Zero Mission:
X: Zero, what's the situation?
Zero: The Mavericks that we had destroyed before are rampaging throughout the island. What has been happening on this island? X, you check out the route below.
X: Roger that. Stay alert, Zero. See you later!

Zero: Humph! Why don't you come out and face me?!

Zero: Are you alright?
X: Let's go up for now so that we can contact Iris.
Zero: Agreed. But, I wonder what they are plotting...

Both:
Iris: X! Zero! We've just received...
Zero: What is it, Iris!?
???: Is it you....? ..... Who had broken into my island?
X: Who are you!?
???: I am Soul Eraser. I erase the souls of evil Mavericks.
Zero: That can't be! What do you really do!?
???: It takes courage to ask someone like me a question like that. Interesting.... Well then, let's play a little game. There are eight guardians on this island. Retire all of them, and then I will battle you.
X: These silly games are pointless.
Zero: It seems that retiring eight might be easier than persuading one.
???: You're very quick, Zero. My name is Gareth. Don't forget it!
Iris: Gareth.... I can't find any data on such a Reploid in out data base. Plus, we have found unfamiliar items...
Zero: We have also found DNA data that was draining out of the enemies.
Iris: They seem to have been resurrecting enemies by somehow utilizing DNA.
Zero: They are erasing the Reploids' DNA in order to create items?
Iris: It seems so. A Reploid's DNA is like that of a human's soul. From now on, let's call it a DNA Soul. We may be able to create something useful from Mavericks' DNA Souls.
Zero: We can't leave Maverick's Souls alone.
X: We must also find the souls of the erased Reploids... Let's gather the DNA Souls!

Berkana: They have been very entertaining!
Gareth: It is unwise to allow them to act on this island. They should be terminated immediately...
Berkana: Not yet, I want the data on the Maverick Hunters. The more they fight, the stronger they would become thus better data would be acquired.
Gareth: we have acquired enough DNA Souls. We don't need anymore.
Berkana: You must have noticed how dangerous it is to fight both of them at the same time.
Gareth: True. It is too dangerous to fight them at once.
Berkana: Let's enjoy watching them for a while. One of the guardians may get lucky and destroy them.
Gareth: It is very unlikely... But if you say so....
Berkana: I can hardly wait to meet them. Hee hee hee.....

X Mission:
Dr. Light: Enter this capsule. Take this Head Upgrade. This Head Upgrade will give you the ability of the Head Crush and allow you to crush certain blocks.

Dr. Light: Enter this capsule. Take this Leg Upgrade. The Upgrade will enhance your mobility and enable you to dash while jumping. You'll also be able to dash upward.

Dr. Light: Enter this capsule. Take this Arm Upgrade. This Upgrade will increase the amount to be charged. You can shot tow charged shots in a row. The two consecutive shots become a wide shot!

Dr. Light: Enter this capsule. Take this Body Upgrade. This Upgrade will increase your defensive ability. Utilizing the energy from damage, you can unleash the GIGA CRUSH!

Zero Mission:
Dr. Light: Enter this capsule. Take this Head Upgrade. This Head Upgrade will allow you to crush certain blocks...

Dr. Light: Enter this capsule. I'll increase your defensive ability and you'll receive less damage....

Dr. Light: Enter this capsule. Take this Led Crush. This Upgrade will allow you to crush certain blocks.

Dr. Light: Enter this capsule. Take this Zero Final. This is the most powerful weapon and will destroy almost any enemy.

Both:
Gareth: Splendid! I'll be waiting for you in the Reploid Research Laboratory! You know where that is....
Zero: I'll put an end to this soon!
Iris: Wait a second. I believe the laboratory is a very dangerous place.
Zero: I know, but we have to go.
Iris: Yes. I'm not going to stop you. Just please take this device. With this device, you can execute a Player Change at anytime by pressing SELECT.
X: All right, Iris.
Zero: I will trust his unknown potential power! Let's go, X!
X: I'll get the DNA Souls back! You're going down Soul Eraser!

X Mission:
Berkana: Hee hee hee! I've been waiting for you, boys. Let me show you the ultimate beauty that can only be realized by gathering DNA Souls. You will learn that I am the strongest!

Berkana: Welcome, boys.
X: Be quiet!
Berkana: You are very cute, even when you're angry! I didn't take Reploids' lives for no reason. Their sacrifices helped to make us stronger.
X: How dare you! That is no excuse!
Berkana: It is pointless talking with you here.

Zero Mission:
Gareth: I anticipated that you would make it this far. I will delete both of your souls!

Gareth: Your reputation is well earned. Sorry about the unworthy games! But just so you know they were Berkana's idea!
Zero: How dare you use the word unworthy?! How many Reploids have been sacrificed in your evil plan?
Gareth: Do not misunderstand me. It was an honor for them to have been chosen as experimental samples. It is as honorable as it gets for mean-spirited Reploids.
Zero: I'm wasting my time talking to you! I'll finish you within the blink of an eye!
Berkana: This is not over yet!

Both:
Why don't you come to Gareth's or my room so that we can relax and talk? My room is above here, while Gareth's is below. The decision is up to you.

X Mission:
X: Zero! It's better for us to separate here!
Zero: Roger that.
X: See you later, Zero! And good luck!

X: I'm coming for you, Berkana!

Berkana: Finally, we are alone.
X: Release the DNA Souls of the Reploids!
Berkana: I admire your speeches. But now, allow me to test the result of my experiment on you. Let me see who is the strongest Reploid! This is my final experiment!

After the battle, X felt the DNA Souls being released. Now the Reploids would return to normal. On his way, various memories flash through X's mind. The most dominant ones are the memories of Zero. Zero should have finished his mission by now. X thinks that he can stand up to any difficulties with his partner and friend Zero. While he thinks like that, he can't help but think of new challenges to face with his friend.

Zero Mission:
Zero: Are they running away again? I'll follow them wherever they go! X, let's separate here!
X: Okay, I'll take Berkana.
Zero: See you later, X.

Iris: Zero! Stop a minute and think about this! If you separate, you are walking into their trap. Why don't you fight together!?
Zero: You don't need to worry. Even though we are far away, I have a feeling that I've been protected by his power. We'll get through this.

Gareth: How very impressive.
Zero: No more words! Let the battle begin!

After the battle, Zero assisted in releasing the DNA Souls. Now the Reploids would return to normal. He has no doubt that X has finished his mission now. Zero and X have faced and fought through many difficulties together. As long as X is with him, Zero can do anything. Though he doesn't express it, Zero believes this with all his heart. This is something that will never change.

Iris: GOOD JOB! You're cleared the game! If you save the data here, you can utilize the saved data for another mission. Please be sure to save and try a new mission!

Iris: GREAT JOB! You have cleared two missions. You deserve a Special A level Hunter! But still I feel uneasy.... I wonder if we really did restore peace.

Xtreme Mode:
Sigma: Hmmm.... You are the ones who made that noise!
Zero: Sigma!
Sigma: But this time, I have to thank you for doing that. Actually, Berkana went too far. Although, she did help me by keeping me entertained for a while. Hee hee hee.
X: It was you who started the incident! Sigma!
Sigma: Now is not the time for talk, now is the time to destroyed! You know, that I'm going to destroy you!
Zero: How dare you!
Sigma: Go for it! Fu fu fu, Bwah ha ha! I'll be waiting for you. Bwah ha ha ha!

Sigma: Hee hee hee. I'm pleased to see you. Now I'll delete your soul forever!
Sigma: It seems that I underestimated you.... The play time is over.... Now I'll bring this to an end....

X: Are you all right? Zero?
Zero: Yeah. I am. Hey, look at that!
X: The DNA Soul are returning! The hollow Reploids will come to life!
Zero: Probably.... Everything is over, now.
Iris: X! Zero! The hollow Reploids are coming to life one by one!
Zero: Iris, rescue the Reploids in cooperation.
X: Let's go Zero! We have to express our thanks to Iris.
Zero: Right. She was very helpful. I feel sorry that her first job as a Maverick Hunter was like this. The Colonel will blame me.
X: The Colonel? But I believe the experience will be helpful when she returns back to the Reploid Force. Anyway, let's go back. We're done here.

Iris: SUPREME JOB! Now that Sigma has been defeated, true peace has been restored. So now I have a present for you! This is an awesome mode where you fight against 8 bosses. How fast can you defeat them? Good luck!