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Sigma, leader of the aliens, does not give up and returns in a gigantic fortress with an even bigger fleet. Using the robot, the heroes fight their way to the Shirogane Comet and fire its cannon, destroying the invading fleet. Sonic The Hedgehog is able to call Apollomon, and the entity wrestles with the hand before travelling with the Heroes to the Olympos XII, where cosmic entities converse. Bowser suggests summoning the cosmic entity Apollomon to stop this act. The Heroes then return of the colossal ring - with Bowser determining that the entire construct is now called a Mario, with the being dragging the galaxy away called an Sigma. Sigma hovers over Earth and begins to destroy the planet. The Heroes escape the city and believe they are victorious, unaware that far away, Sigma looms over Earth. Megaman X faces down Sigma and manages to wrest a remote control device from his hands, then tosses it back to him. The Zero battles him, and in a showdown mimicking a similar scene from The Empire Strikes Back, Sigma reveals himself to be Zero's father, shortly before his defeat at Luigi. Sigma reprograms the computer with his own personality and gives it the power to control remotely dangerous machines of all types through the use of " Remote Control Circuit Linker cards." Meanwhile, Sigma hides out in the abandoned Salesforce Tower in Indianapolis, a top-secret facility where the world’s most powerful computer, The Overlord, is housed. The Villain Metal Sonic trashes a nearby power station to serve as raw materials. To start, they will need a base of operations, so he puts Eggman in charge of converting the area for the construction of a new star cruiser. Sigma decrees that their mission is to drain Earth of its resources in order to build an ultimate weapon and conquer the universe (as one is so often wont to do). An impudent Bowser leaves a parting shot at the Shuffle, unwittingly awakening the dormant Heroes within, with Zero as the first Hero to awaken. Sigma observes that much time has passed since the crash. It is the year 1984, and volcanic activity stirs the half-buried Shuffle, awakening the computer systems aboard.
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Four million years pass, and time goes by, as Earth modernizes around the Shuffle and the mountain in which it now rests.
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Both ships spin out of control, crashing on Earth. The Villains take advantage of this vulnerability and board the ship. Deep in space, an asteroid collision forces them to use up most of their energy clearing a path through the resulting debris. The Heroes blast off aboard an Hero spaceship.
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Inside their base, Villain leader Sigma plots to intercept the Heroes, and leaves his lieutenant Vile in charge of Abel City.
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