Prologue In the year 22XX AD, a mysterious mineral known as Force Metal was extracted from the fragments of a meteor that landed in the Pacific Ocean. Technology based on the metal revolutionized the field of Reploid engineering. The Federation built Giga City, an artificial island, near the meteor site for the explicit purpose of mining and smelting Force Metal.

Everything seemed to go well, until a band of renegade Reploids armed themselves and launched a rebellion on the island. They banished all humans and demanded that the government recognize Giga City as an independent Reploid state. This new Rebellion Army and its leader, Epsilon, were all branded Mavericks for this deed.

After the first team of Maverick Hunters was annihilated or otherwise subdued by the Rebellion Army, Colonel Redips sent in a special team composed of X, Zero, and Shadow. If they failed their mission - arrest Epsilon and quell the Reploid insurrection - the Federation would have no choice but to declare all-out war on Giga City and the Rebellion Army.

Chapter 1: Infiltrate Giga City! X, Zero, and Shadow teleport to the outskirts of Giga City to investigate an energy reading in the Lagrano Ruins. The trio are separated by a mysterious explosion, but they continue towards the top of the structure. X and Zero meet up near the top when they are suddenly attacked by Hippopressor, which they destroy.

Upon making it to the roof, X and Zero find Shadow faced with Epsilon. They begin to arrest Epsilon, but Shadow turns on them, revealing his true allegiance to the Rebellion Army. The Rebellion cadres - Scarface, Botos, and Ferham - also reveal themselves, and the Hunters realize that they've been led into an ambush. Zero attempts to strike Epsilon, but is overpowered and sent flying by the cadres attacks. Now alone, X finds himself with no other choice but to flee, leaping off the roof and into a chasm below. Ferham begins to give chase, but Epsilon stops her, well-aware that X will return.