On a transport heading for Neo-Arcadia, Leviathan awakens in the medical center, having her wounds repaired though she still feels the pain of them. Wanting to sit up, Leviathan stops as she sees her wrists bound to the railing on her gurney.

"Hey, what is this?" Leviathan states in protest. "Hey, I'm awake; let me up!" At this commotion, a pantheon rushes inside to address her.

"Master Leviathan, it's good to see you conscious. We found you in the ruined city riddled with injuries." The pantheon reports.

"Fine, now let me up. I have to go find that Maverick."

"I'm sorry, but I have orders to keep you confined here."

"What?! On who's authority?!" Leviathan shouts in frustration.

"Mine." The pantheon quickly moves aside and the source of the voice walks in; a Reploid with a black and white body suit, a white mask that covers the upper part of his face, a black and white helmet with two prongs jutting back, a red scarf around his neck and yellow bands on his ankles, thighs, wrists and forearms.

"Phantom..." Leviathan declares in a subdued voice.

"Would you mind telling me what happened down there now that you're awake?" Phantom asks with his arms crossed, staring at Leviathan.

"I engaged the Maverick after he made it into the Disposal Factory and..." Leviathan hesitates before continuing.

"You lost." Phantom ends her sentence.

"...yes."

"May I ask how that is possible?" Phantom asks, clearly upset.

"He...was stronger than I thought." Leviathan states, hanging her head in embarrassment.

"You didn't follow the Master's orders, did you?"

"Phantom, I didn't know that he had that much energy within him! Besides, I was out of the water; he got lucky." Leviathan retorts.

"NO EXCUSES." Phantom raises his voice. "You failed, plain and simple."

"Fine, let me out and I'll take care of it!"

"No, I'll take care of it. You're going back to Neo-Arcadia to give your report to the Master and await further orders."

"Hey, you can't do that!"

"I just did." Phantom declares and leaves Leviathan still restrained to the gurney. Now alone, she takes her time to seethe.

"Zero..."

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The Ancient Laboratory

Through the Trans-server, Zero arrives back at the ancient lab.

"I made it." Zero asks through his communicator.

"Good. Alright, there should be a hub in the room where we found you; you need to go there and retrieve any and all data from within it and bring it back to us. Be careful though; we're picking up several enemy markers, they must be here to gather any data on you as well." Ciel states the mission instructions.

"Copied. I'll give you a call if anything comes up." Zero ends the communication and exits the room.

Approaching the shaft that he and Ciel fell down through to escape the pantheons, Zero recalls an old technique; he jumps up the shaft by kicking up each wall until reaching the top. Now on the top level, Zero looks down the eerily quiet halls and makes his way towards his capsule chamber. At that moment, a small, red spider-like mechaniloid lands on Zero's left shoulder and he grabs it. The spider screeches at Zero before trying to bite him and the latter crushes it in his hand. After this, a small swarm of spiders emerge and converge on Zero.

"Zero, run!" Ciel shouts in alarm and Zero quickly runs down the hall towards the capsule chamber, shooting at the screeching swarm every so often to slow it down. "You're almost there, keep moving!"

"I see the gate, it's still open!" Zero shouts as he spots the entrance. A few of the spiders catch up to him, climb up his torso and begin biting him. Resisting the damage, Zero makes it inside and blasts the control panel to the gate, closing it and stopping the swarm. Now in the clear, Zero tears off the spiders on him and begins crushing and stomping on them until they've all been eliminated. "Ok...I hate spiders." Zero, in an almost breathless tone, resentfully states. "Ok, I'm back in this room of mine; now what?"

"Ok, now I need you to access the hub next to your capsule, or what's left of it, and gather any and all data within." Cerveau instructs. "Your memory banks should be large enough to hold all the data in the mainframe. Just install the decryptor that I gave you."

"Alright, give me a sec." Zero walks up to the hub and installs the decryptor, bypassing any security and firewall. "I'm in; let's see what we've got." Once accessed, Zero manipulates the keyboard and taps the crystal on his head to download the data, only for nothing to be found. Though initially surprised, Zero uses the search engine to locate anything at all (Search: Zero, timeline, projects and even Mega Man X), but the search yields the same answer: No Results Found. "Damn it...Ciel, Cerveau; there's nothing here. I think Neo-Arcadia beat us to it already."

"No...ok, Zero; come back to base. We'll try and figure something out from our end; maybe we can hack into their mainframe from here." Ciel remorsefully states.

"Wait, Zero!" Cerveau cuts in, surprising Zero. "I'm picking up a large energy signature in that room, I don't think you're alone."

On cue, a large, yellow and aquamarine ball falls down, forcing Zero to dash away to avoid getting crushed by it. The ball opens its parts and two arms and legs extend out, along with an elephant like head that glares at Zero, revealed to be another Mutos Reploid.

"You were on the spot, Cerveau..."

"Zero, so you have arrived. My name is Maha Ganeshariff; you are wanted for crimes against Neo-Arcadia. "The Mutos Reploid, now known as Maha Ganeshariff, declares to Zero. "Will you comply?"

"Zero, I'm picking up several terabytes of information coming from within him; I think he has the data!" Ciel states in realization.

Smirking, Zero draws his saber and spreads his arms out at his opponent. "Waived."

"Then let termination be your outcome!" Maha waves his trunk sideways, releasing several explosive charges at Zero. He responds by dashing towards his opponent, slashing at several charges to keep them from detonating while simultaneously avoiding the explosions. Getting close, Zero slashes at Maha and the former responds by deviating the slash downward with his arm and backhanding Zero towards the rubble and he immediately recovers. "You will not escape; it's over-" Maha is cut off as Zero boosts towards him, knocking him down to the ground after kicking his head before deviating from the ground to stab him. Maha immediately extends his trunk towards the ceiling, escaping from Zero's attack and using his body like a wrecking ball to strike Zero, lodging him on his surface. Maha, in his wrecking ball mode, runs Zero against the walls and the latter uses his saber to try and cut through the formers chassis, despite the damage he is currently receiving. Running the saber into a newly made breach, Zero uses it to keep himself steady and he fires off several shots from his blaster at Maha's trunk, finally dislodging them both as they fall to the ground away from each other.

"Oh...man..." Zero painfully gets up off the ground from both damage and friction burns. At that moment, Maha regains consciousness and throws his tusks like boomerangs at Zero with one of them lodging itself in his left shoulder.

"Did you think it was over?!" Maha Ganeshariff shouts in anger as he shoots several energy rounds from his trunk as Zero uses his saber like a makeshift shield to block them. Eventually, Maha bats away the saber with his trunk, restrains Zero with it and brings him up. "Where is the Resistance Base?"

"What Resistance Base?" Zero defiantly states.

"Very well then..." Maha grabs Zero and retracts his trunk, tightening his grip as Zero struggles. "Zero, Crimson Maverick, as part of the Resistance that defies Neo-Arcadia; you are hereby labeled as a terrorist. The sentence for these affronts is termination. Is there anything to say in your meager defense?"

"Yeah...you talk too much." Zero grabs the tusk lodged in his own shoulder and tears it off before jamming it into Maha's breached chassis. Exclaiming in discomfort, Maha drops Zero as he reaches for his own wound while the latter pulls out his blaster and begins charging it; having covertly placed one of Maha's discarded explosives on the other end.

"No...NO!" Maha realizes too late what Zero's plan was as the latter fires off a charged shot at the tusk, obliterating Maha Ganeshariff. As the smoke clears, Zero gets up off the ground and observes the scattered remains of Maha Ganeshariff.

"Guys, it's done." Zero speaks through his communicator, clearly exhausted from the ordeal.

"Excellent work, Zero." Cerveau answers in a relieved tone. "Don't bother downloading the data now, bring back his internal mainframe and we'll do the rest back at the base."

"Got it, I'll be back in a moment." Zero puts his weapons away and looks through Maha Ganeshariff's remains until he finds the large mainframe; resembling a large black box with red circuit boards on all sides. "I found the mainframe, now- what?" Zero becomes distracted by a steadily growing in volume and speed. "Is that...?"

"Zero, you've got to get out of there RIGHT NOW!" Ciel shouts in alarm and Zero grabs the mainframe before running towards the entrance to the chamber, cutting through it with his saber. Running down the hall, Zero swipes at the spiders in the way as he heads for the shaft and as soon as he drops down it, Zero kicks the door open and immediately uses the Trans-server to teleport back to the base. The beeping within Maha Ganeshariff's remains finally stops and the bomb hidden inside detonates, completely destroying the ancient lab.

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Resistance Base

Zero returns via the Trans-server and both Ciel and Cerveau catch him before he collapses, with Zero catching the mainframe before it falls.

"Zero!" Ciel exclaims happily.

"Goodness, you're looking a bit worse for wear." Cerveau comments, looking over all the damage that Zero had sustained.

"You should see the other guy." Zero quips, smirking slightly before bringing up the mainframe. "I think this is what you wanted."

After making sure that Zero can still stand on his own, Cerveau takes the mainframe. "Yes, the data should be in here. Ok, I'll take a look at and in the meantime, you should get some rest; I had a power charger installed in your room, you can use that to repair damage done to your body while you sleep."

"Got it, thanks Cerveau."

"Come on Zero, let's get you over there." Ciel continues to offer her shoulder to Zero as they walk to the latter's room so he can rest.

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Hours later

Zero awakens reinvigorated and makes a beeline for Cerveau's lab. Though when he enters, Cerveau has a glum expression.

"Cerveau, what's wrong?"

"Ah Zero, good to see you up and about." Cerveau flatly greets. "I'm afraid I have some bad news; the data mainframe was damaged, no doubt when you destroyed that Mutos Reploid. Well over 80% of the data was lost."

Though initially stunned, a disappointed Zero sits down at the table with a heavy sigh. "I don't believe this; so I just ruined my chance at finding out more about myself and I can't even find out by checking the lab again because there's NO lab anymore?"

"Calm down, Zero. Don't blame yourself for any of this." Cerveau brings up a screen and a crate from behind his desk. "There is a bit of good news; I was able to construct some new weapons for you from the data, or rather old weapons; according to the data, you've used them before."

"Really?" Zero asks and Cerveau opens up the case in front of him. Standing up Zero pulls out a white rod-like device with a flat end on each side with a black tip. Holding the center of the rod, it extends into a lance like weapon with a green spearhead on one end. "Whoa."

"Nice, huh?" Cerveau asks with an air of self-importance. "I call it the triple rod. Its head can extend a total of three times, hence the name. Make no mistake through; with your strength, it can bust through several opponents. The other end can activate its own spearhead and does the same as the previous one, go ahead and get creative. Now, go and check the last one in the case." Cerveau instructs as Zero places the triple rod on the table before taking out a white disk-like device that the former has the latter place into his left forearm. Once done, it expands and extends a rotating green, sawblade shaped disk. "That's the shield boomerang. As its name implies, it can block energy shots and can be thrown like a boomerang, cutting through enemies before it comes back to you."

"Huh, not half bad. Thanks Cerveau." Zero, feeling somewhat better after learning that he lost most of the data. "These will definitely come in handy during missions."

"And there's some more; see, while most of the data was lost, I actually managed to find pieces here and there and I found out something. Zero, while it's known that you were in that capsule for a little over a century, you actually entered on your own volition."

Blinking twice, Zero becomes stunned at this information; why did he enter that capsule of his own free will? "I what?"

"Yes, you were in there because you wanted to be inside. I couldn't begin to tell you why, unfortunately."

All I know is that it was roughly before the end of the Maverick Wars."

"Well, I guess it's a clue. Do you know who was administrating that lab I was in at least?"

"No, I'm sorry Zero." Cerveau remorsefully answers. "I think the only way for your memory to be restored at this point is if you stimulate your mind. It's a long shot, but I'll try to locate as much as I can about you in any surviving records."

"I appreciate that." Zero nods at Cerveau with a half-smile before picking up the triple rod, retracting and storing it behind his waist. "I should be going now. If anything happens, you know where to find me." Without another word, Zero walks out of the lab and towards the Resistance proper. Now alone, Cerveau looks at the screen and ponders.

"What exactly were you doing in that lab, Zero?"

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With nothing to do, Zero wanders through the base, receiving scattered salutations from the members and rescued Reploids, much to his surprise.

"Zero!" Turning to his right, Zero spots Alouette running and calling out to him. "You're back!"

"Hey Alouette." Zero amicably greets his new friend. "What can I do for you?"

"I want to show you something; one of the Reploids you rescued brought some things from Neo-Arcadia before he was apprehended. Come on!" Alouette excitedly grabs Zero by the arm and leads him to an elderly looking Reploid with a long green gown, long white beard and eyebrows and a brown cane seated next to a table. "Andrew, this is Zero!"

"Ah yes, good to finally meet you Zero." Andrew greets in a tired and elderly voice. "I never got to thank you for freeing us from that disposal center."

"It's alright. I'm just glad I got to all of you in time." Zero states.

"Andrew, can I show him?" Alouette asks and Andrew complies by handing her a bag filled with small paper sacks. "Look Zero; seeds!"

"Seeds?" Zero asks with his head cocked to the left.

"Yeah, Andrew brought them and said he'll teach me how to plant these. That means that Ciel will have fresh vegetables to eat and not just those old military rations!" Alouette excited states. "Not only that, but there are also flower seeds; I'll finally be able to see what they looked like in real life and not just in records!"

"Yes, I also know how to bake; with the proper ingredients, I can make bread for Miss Ciel. It's the least I can do for your help." Andrew adds, gently patting Alouette's head.

"That's very nice of you." Zero states with a friendly demeanor. "I actually forgot that Ciel is the only human in the Resistance Base; she needs food and not energy crystals, heheh."

"Hmm, why is she the only one anyway?"

"You know, that's a good question, Andrew..." Zero ponders with his arms crossed.

"Zero, look!" Alouette brings Zero out of his thoughts and shoves the sacks of flower seeds in his face.

"Whoa! What's up?"

"There are so many kinds of flowers! I recognize all of them, read the names!"

"Ok ok, let me see them then." Zero takes the sacks and begins reading the labels. "Alright, there are roses, tulips, ooh orchids, cherry blossoms, lilies, chrysanthemums and...irises." Zero's expression turns into one of uncertainty after he reads the names, especially the last one. "Irises...irises...Iris..." Zero repeats several times, almost as if he were in a trance.

"Zero, your face..." Alouette speaks up, pointing at Zero.

"Huh?" Zero snaps out of it and reaches up to his face, stroking what feels like moisture below his eyes, confusing him.

"Zero, are those...tears?" Andrew asks, just as perplexed as Zero.

"What's wrong, Zero? Do you, maybe, not like irises?"

"Uh...I don't know what that's about." Zero wipes his eyes with his free hand before handing the seeds back to Alouette. "Here, keep them safe for when it's time to plant them."

"Zero, are you sure you're ok, lad?" Andrew asks.

"Yeah, I think I'm still a little tired from the whole ordeal. Don't...worry." Zero answers with yet another half-smile. Despite his assurances, Zero felt something when he said the word "Iris" out loud. He was sure that it was...sadness. But why...? Eventually, Zero is once again brought out of his thoughts as a bell started ringing and many of the Reploids scramble towards another room; Zero stops one of them to get answers. "Hey, what's going on?"

"Neo-Arcadia! There's a state of the union in Neo-Arcadia starting right now!" The Reploid quickly answers before running off with the others. Zero decides to join them, telling Andrew and Alouette to stay put as he runs off to a large room with several seats and a big screen covering the north wall. Zero sits at one of the front seats and Ciel joins him.

"Ciel? They said something about a state of the union, what does that mean?"

"They want to address some big information to the citizens of Neo-Arcadia, specifically The Master." Ciel answers.

"The Master? You mean..."

"Yes, Zero...Mega Man X."

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Neo-Arcadia

In the streets of a metropolitan area of Neo-Arcadia, thousands upon thousands of human citizens walk down them with several hundred pantheon troopers at their sides to prevent any and all commotion. Their path leads them to a city center surrounded by many plants and lush green grass and at the front of it is a pyramid like structure made of marble and a massive tower that extends towards the heavens behind it. As the people wait patiently, eight figures of varying sizes wearing white robes that obscure their features sit at the bottom of the pyramid. Above them, the Four Guardians of Neo-Arcadia arrive in sequence; Harpuia, Fefnir (a Reploid with red and white armor, a large red breastplate, shoulder pads and boots, two pairs of yellow fang like spikes at the top and bottom of his red helmet and two red cannons on his back), Leviathan and Phantom. The four sit at the seats above the 8 robed figures but below the top of the pyramid. After what felt like an hour of tense waiting, a large squadron of pantheons arrives and position themselves on a stretch of path above and behind the pyramid as a large and extravagant transport that almost resembles an ark flies down and lands at the other end of the path. The gate slowly opens and the pantheons kneel down as a lone figure wearing a dark blue robe walks down the path, his footsteps echoing in the quietness of the area. Finally, the figure stops at the top of the pyramid and is revealed to be wearing a dark blue helmet with light blue fringes that frame his face, a red crystal at the front of it and matching red eyes. As he arrives to his spot, the Four Guardians rise up and say at the same time: "All hail Master X!" The crowds cheer in reverence to Master X.

Raising his hands up to the air slowly, Master X calms the cheers until they gradually cease. "People of Neo-Arcadia, I thank you all for your attention. Earlier today, the Mavericks have attacked and destroyed an installation on the outer limits of Neo-Arcadia, destroying a large number of our forces. Along with these disturbing events, an abandoned laboratory was destroyed by the Mavericks as well. However, this was no mere act of violence; the Mavericks have unleashed an ancient Reploid and in doing so, have destroyed the lab to erase any and all evidence. I am ashamed to say...I know this Reploid very well as do you all, he was my brother in arms; Maverick Hunter Zero." Master X announces, much to the crowd's shock. "Our contacts indicate that Zero has joined the Mavericks and has plans to endanger our way of life. I have summoned you all here today because I do not wish to keep this information from the people I have sworn to protect. It weighs heavy on me; but as much as it pains me to say, I henceforth declare Zero as Maverick and he will be treated as such. Though we are in the midst of an energy crisis, my resolve has never been stronger; I will make sure that Zero answers for these offenses, as well as the Mavericks he has allied himself with. Citizens of Neo-Arcadia, rest easy knowing that your watchful protectors will wipe out this plague; we will prevail!" Master X concludes his announcement and the people erupt in thunderous applause.

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Resistance Base

"However, this was no mere act of violence; the Mavericks have unleashed an ancient Reploid and in doing so, have destroyed the lab to erase any and all evidence. I am ashamed to say...I know this Reploid very well as do you all, he was my brother in arms; Maverick Hunter Zero. Our contacts indicate that Zero has joined the Mavericks and has plans to endanger our way of life."

"What?!" Zero, surprised by this false announcement, rises immediately from his seat, shocking a few of the Reploids with his outburst. "That's a lie! They destroyed the ancient lab; I had nothing to do with that and neither did any of you!"

"Zero, please calm down." Cerveau arrives to try and placate Zero's anger.

"Cerveau, they can't do this! ....can they?"

"I'm afraid this is Neo-Arcadia's propaganda; they call us Mavericks to paint us in a bad light when in actuality we're trying to survive however we can. The people believe those lies because Mega Man X is the founder of Neo-Arcadia after the end of the wars. He created it as a beacon of hope for the survivors of those conflicts; both Man and Reploid." Cerveau explained.

"Then how can he do this to his own kind?! Energy crisis or not, he's wiping out innocent Reploids in droves! Ciel, there has to be something we can do- where did she go?" Zero looks to his seat and sees that Ciel is no longer next to it.

"She left ahead of everyone else; I think she went to her room if you want to speak with her. But Zero, try to cool down before seeing her."

Huffing in frustration, Zero walks out of the room and towards Ciel's quarters.

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Taking Cerveau's suggestions into account, Zero calms himself down before knocking on the door to Ciel's room.

"The door is open." Ciel states from inside and Zero walks inside. Ciel's room was a quaint one; a closet filled with clothes, a desk with a lamp and writing paper, an LED light on the ceiling and a bunk bed where Ciel was seated, using a laptop with a serious expression. Ceasing her typing for a moment, she looks up to address Zero. "Oh, hello."

"Ciel, are you ok?"

"I'm fine; just working."

"On what?"

"This." Ciel turns her laptop screen to face Zero.

"New energy source?" Zero reads the title out loud.

"Yes, I've been working on a new type of energy for a while now. My hope is that once a new energy is discovered, then it will bring an end to all this senseless fighting and disposal of innocent Reploids. However, progress has been slow recently; I just don't have the proper equipment for adequate research."

"Did...you hear about what X said?" Zero hesitantly asks.

"Yes. That is precisely why I can't afford to waste any time; the sooner I can find a new energy source, the sooner this all ends. I hope..."

Sensing Ciel's somber tone, Zero sits down next to her. "Ciel, is this the reason you're in the Resistance?"

Breathing deeply, Ciel looks at Zero after shutting her laptop. "Zero, there's a lot to answer for; I have to do this to make things right."

"But why? Why is any of this necessary? If X created Neo-Arcadia many years ago as a safe haven for everyone, then why is he taking this extreme?"

"Things change, Zero. People change." Ciel states before looking down in sadness. "People change..."

Zero has an unreadable expression at Ciel's words, eventually deciding to pat her back softly. "Ciel, it's alright."

"Zero, if it's fine with you, I'd really like to be alone now..." Ciel quietly requests and Zero concedes, leaving her room and making his way towards his own room, having nothing more to do today. As soon as he steps inside, Zero's head begins to throb and he grunts in discomfort as another memory surges.

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Unknown point in time, Zero's POV.

Zero looks over a destroyed facility from a rocky terrain.

"It's over, but for how long?" Zero asks, still weary from a battle.

"I don't know." A voice answers from Zero's right side and he spots another figure. Though blurred in his memory, he sees that this person is a blue Reploid. "But, you taught me to keep fighting, Zero. So, that's what I'll do."

"Heh, you've come a long way since Sigma's first incursion. I knew you had the strength necessary."

"I couldn't have done it without you, Zero. You taught me to find a reason to fight and now I know what it is." The blue Reploid declares.

"Oh yeah? What's that?"

"I'll keep on fighting for the day when I don't have to anymore. When humans and Reploids can finally live in harmony, without discrimination and without conflict. I'll make that a reality; somehow, someway."

"Is that so? Well, I think I'll stick around to help you out with that. You've got a big heart, in a manner of speaking, so I need to be there to keep you out of trouble." Zero states in an almost jovial tone.

"I wouldn't have it any other way. Thank you, Zero." The blue Reploid happily states.

"No." Zero reaches over and pats the blue Reploid on his shoulder. "Thank you, Mega Man X."

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Zero's room

The memory ends and Zero hyperventilates, recalling one of the conversations he had with his old compatriot; Mega Man X. If this truly is how he remembers him, then how is it possible that after, supposedly, founding a safe haven like he wanted then why did he go back on his word with no discrimination and no conflicts? As far as he was concerned, Zero's old friend lied to him. Getting up from his knees, Zero sits down on his bed and begins pondering his next move and after an hour later, he comes to a conclusion; he must stop Mega Man X. He will do everything he can to help the Resistance stop Neo-Arcadia's oppression, find a way to help Ciel find a new energy source and confront Mega Man X to ask him the one question that is hovering over his mind...

"Why are you doing this?"

To be continued

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Author's Note: Alright, more plot. To all the fans reading this chapter, you will have no doubt noticed the references to the X series and yes; they are not simple references. They will play a part in later chapters of this story and the future novelizations because I feel that Zero needs to adequately conclude some of these plot points that were unfortunately not done in the game series. Alright guys/girls, take care. :)