With Hunter Base secured, X and Zero returned to Dopple Town to carry out the mission. Fortunately, Zero was able to destroy Mac and free X, and together they stopped the siege on Hunter Base. X and Zero returned to the headquarters to immediately to stop them, where X was betrayed and kidnapped by their former ally Mac. Hours later, however, an emergency contact was made by Hunter Base, revealing they were under direct attack from Doppler's forces.

The call went out to X and Zero to infiltrate Dopple Town, destroy the rioting Mavericks, and bring Dr. Doppler was the mastermind behind the chaos, and soon he declared war on the world and put Dopple Town under martial law. All the Maverick Hunters' intelligence indicated that Dr. Doppler began to riot, revealing that his so-called vaccine was little more than a placebo. Ī few months later, the Mavericks who were supposed to have been neutralized by Dr. Doppler guiding them, the world seemed ready to enter a new golden age. Many advanced Reploids and reformed Mavericks gathered near their new mentor and founded ' Dopple Town', a perfect utopian community. With this discovery, he claimed to have synthesized an anti-viral defense that was effective even against the Sigma Virus, and also to have developed the means to suppress irregular behavior in Mavericks, causing virus-infected Reploids to return to normal. Doppler finally identified an advanced virus that was forcing Reploids to go Maverick, dubbing it the Sigma Virus. Fortunately, the genius Reploid scientist Dr. Despite this, Maverick activity continued. In the year 21XX, Sigma's rebellion was finally crushed thanks to X, Zero, and the Maverick Hunters.

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