In the year 21XX....
Reploids, powerful living robots with true free will and human emotions, have spread across the globe. But among the Reploids are aberrations, ones who turn on mankind, Mavericks. The Maverick Hunters have been formed to track down, contain, and if necessary destroy Maverick Reploids.
Over the years, the war against the Mavericks has had a heavy price. Mankind had been forced to live underground as the Earth's surface was rebuilt after the catastrophic fall of an orbiting colony, and now plans have begun to terraform the moon, beginning the expansion into space.
As part of this expansion, a new generation of Reploids has been created, with the ability to replicate other body forms as needed. With their advanced powers, this new generation has constructed the Orbital Elevator "Jakob", a structure hundreds of miles high that can easily transport cargo and passengers into low orbit within minutes either via electro magnetic rails on its outside, or the central lift platform in its center. Shuttles make runs between the top of Jakob and the gateway space station, which serves as a supply point for the final journey to the new moon bases.
Recently, the Jakob Project has come under attack. Mavericks have attempted takeovers of the Orbital Elevator, and the bases world wide that supply its raw materials and programming. Veteran Maverick Hunters X & Zero are dispatched along with the rookie Hunter Axl to investigate the attacks and ensure Jakob's safety.

X: X is the final creation of the great Dr. Light, locked away in a diagnostic capsule for a century until he was unearthed by the archaeologist Dr. Cain. He helped Dr. Cain begin production of the Reploids, and stayed a civilian until the first great Maverick rebellion instigated by Sigma, at which part he joined the Maverick Hunters. X longs for the day when Reploids and mankind live in peace together, free from the horrors of war. Until that day, he fights for justice with every ounce of his being, and hopes that each battle will be the last.

Zero: Zero is X's best friend and near-constant teammate in the war against Mavericks. Ironically, Zero was originally created to destroy X, he is the final creation of the mad Dr. Wily, Dr. Light's former assistant turned would-be world-conqueror. Zero resisted his creator's whims, and once freed from the influence of the virus placed within him, became one of the most powerful Maverick Hunters of all time. Zero can sometimes be cold, gruft and incredibly bull-headed, but he never gives up the fight against those who would take advantage of the weak.

Axl: Axl's specific origins are shrouded in mystery, but he appears to be a prototype of the new generation Reploid model, capable of altering his form by using DNA Scans from other Reploids. Axl was pursued by Sigma after he left the Red Alert Organization, and ended up with the Maverick Hunters. Young and headstrong, Axl idolizes X and Zero, rushes into combat eager to prove his worth.

Signas: The commander of the Maverick Hunters, Signas took the job after the original commander retired following the destruction of the Repliforce Army. Signas was extensively trained for command, scoring top ranks in all simulations. Signas leads calmly, directing hunter operations with precision.

Alia: Alia is the Maverick Hunter's top Navigator. Her advice has saved many a life when she has guided the hunter field operatives. She has a broad depth of knowledge, and also studies ancient technology in hopes of better understanding the origins and secrets of Reploid development. A dedicated navigator with a long record of success in the hunters, Alia strives to better herself and provide the best assistance to field operatives she can.

Layer: A new member of the Maverick Hunters, Layer is trained as a navigator specializing in Reploid and Mechaniloid development. Her high processing power allows her to quickly analyze scan data sent back by hunters in the field and determine a target's strengths and weaknesses. Layer is cool and collected.... Most of the time. She seems to get a little flustered when working with Zero, though....

Pallette: A new navigator for the Maverick Hunters, Pallette is a skilled cartographer who is capable of reading the lay of the land, able to detect structural weaknesses, and advise hunters on dangers and vantage points near their location. She also helps maintain the R & D Lab, developing new gimmicks and upgrades for the hunters. Feisty and short-tempered, Pallette hates being ignored.

Dr. Thomas Light: The greatest mind in robotics engineering, his work is untouchable even a century after his demise. Dr. Light pioneered the advance AI with the "Humanoid" robots, the greatest among them the robot children Rock and Roll. Dr. Light continued to work on more advance robotics, in the hopes of protecting mankind from people with evil ambitions, like his former assistant Dr. Wily. Knowing his final and most powerful creation would not be activated until well after his life expectancy, Light created an AI program with his own mind as the template, which designs new armors and advances for X to assist him in his quest to defeat evil.

Lumine: Lumine is a new-generation Reploid, the director of the Jakob project. A young model, Lumine is brilliant, but he speaks in a cold, near-emotionless tone. He has become the target of Maverick attacks in the hopes that he will give up the secrets and control over the Orbital Elevator.

Sigma: Sigma was at one time the best of the Maverick Hunters. Until one fateful day, he went up against a rogue red Reploid.... Zero. The powerful virus contained within Zero was transferred to Sigma during their fight, and in time, Sigma went Maverick, taking many of the best Maverick Hunters with him as he began a war against mankind. Each time Sigma has been defeated, he rises again to torment the hunters.

Maverick File: Vile
Vile was originally a A-Class Maverick Hunter, though during his career he racked up more disciplinary charges for unnecessary force, excessive violence and endangering his team-mates than any other hunter in history. It even hit the point where other hunters were afraid of being put on a mission with him due to his reckless and downright blood thirsty tactics. When Sigma turned Maverick and took many of the best hunters with him on his war against humanity, it was no surprise that Vile followed him willingly. Though his favorite tool in battle was Ride Armors, even on his own he was a powerful hunter.
He was thought to have been destroyed by Zero and X during the first Sigma revolt. Zero sacrificed himself to destroy Vile's Ride Armor, and X defeated him in single combat. Ultimately, both Reploids' remains were recovered from the wreckage of Sigma's base and rebuilt by Maverick agents.
Vile was not heard from again until the riots of Doppler Town a few short years later. Under the control of Sigma, the benevolent Dr. Doppler rebuilt Vile into a more powerful form. Vile's sole drive then was the destruction of X and Zero, rushing into combat. Even backed by his new, high-powered Ride Armor "Brown Bear", Vile fell again to X. Unfortunately, recovery teams sent to Doppler Town after the riots were unable to locate Vile's remains.
Now he has returned once again in his new V-body. Will this be the final duel for this mad ex-hunter?

Alia: I'm picking up Maverick reading near the Jakob facility! All Hunters near Point Galapagos, please dispatch immediately!
X: Roger.

Alia: X... This new Maverick... It's pattern is very unusual. I'd like to do some research on it, so try to pick up plenty of samples.
X: Got it. OK Axl, let's get going!
Axl: Ready when you are, X.
Alia: When you need Axl's help, call him in with a Character Change.
Axl: Better watch out, X. I might just steal your spotlight.
Alia: You two be careful. I'll send Zero over later to give you a hand.

Alia: X, Axl! I've examined the data on that Maverick. Looks like it grabs its opponents and immobilizes them. If you're grabbed by the enemy, call for a Tag Assist and help is on the way!

X: Alia... I got a sample of that Maverick for you.
Alia: I'd like to start analyzing it right away. Bring it to me as soon as you can!
X: Roger. I'm on my way. Axl, I'm counting on you to clean up here.
Axl: No problem, X! This'll be a snap.

Alia: Axl, it looks like you'll need to hover over from the edge to continue onward. To hover, press the jump button again and hold it while in mid-air.

Zero: Axl, pick up the pace! This is no time to slack off!
Axl: You show up late and have the nerve to complain? I can more than handle a few Mavericks all by myself anyway.
Zero: That's the spirit! Let's move!

Alia: Now, you two! The Attack Gauge is full! You can use the Double Attack! It's an ultra-powerful combo! Time it carefully!

Axl: Ha! Piece of cake! Snagged a sample from that Maverick, too!
Zero: Nice work! Now, take it and head back, Axl.
Axl: OK! I'll leave the rest up to you.

Alia: It looks like the entrance to that building is above you. Use the Double Jump to get up there.

X: Sorry to keep you waiting, Zero. How've you been holding up?
Zero: Barely broke a sweat... C'mon! Let's go!

Alia: I've completed my analysis of enemies who use protective barriers! They can completely defend against normal attacks, but you can break their barriers. X's full Charge Shot does the trick, as does Zero's third hit in a combo... And Axl can break barriers with repeated concentrated shots.

Alia: X, Zero... Can you hear me? That Maverick's signal is getting really close now. According to my analysis, the Double Attack should work best on this Maverick. When the Attack Gauge is full, use the Double Attack!

Signas: That looked like a hard fight, but there was never any doubt that you'd come out on top.
 
Pallette: Hello, everyone. Welcome to the laboratory. This is where you can save your progress and develop Chips.

Alia: Let me introduce your new navigators...
Layer: Nice yo meet you, Hunters. My name is Layer. My specialty is analyzing enemy abilities. I hope I can be of use.
Pallette: Hi! I'm Pallette. I'm good at analyzing routes through stages.
Alia: I don't suppose I need to say it, but I - Alia - will also assist in navigation. Before you head into battle, be sure to choose a navigator to assist you. Of course, if you're feeling confident, you can always choose to go it solo.

Alia: Knowledgeable in both stage layout and boss techniques.
Layer: A specialist in boss analysis.
Pallette: Good at analyzing routes, and can uncover hidden ones.