The God's Pest: a Sonic.EXE tale

Sonic and Shadow traverse across South Island, through the Ruined Hills, to the Rusted Spring Yard, and the destroyed Star Light City, before finally ending up at the entrance to Eggman's former Base of Operations: the Scrap Brain Zone. The two heroes race through the Zone, dispatching the leftover Badniks and other security measures before finding themselves in the Final Zone. The room is...empty...quiet...too quiet. 

"Come on out, X, we know you're here!" Sonic yells, getting down into a fighting stance. Shadow listens closely, as all of the sudden, one of the hydraulic presses slams down onto the floor. Sonic and Shadow spin around to see an all too familiar Doctor manning the controls. 

"HOHOHOH! We meet at last, you horrible hedgehog!" Robotnik declares, commanding another one of the presses to drop, causing Sonic and Shadow to lose their footing. "I see you brough a friend  with you! You know what they say, the more the merrier!" 

"Eggman! I should have known you were behind this madness!" Sonic yells back, Spin Dashing into the press, causing Robotnik to lose his grip on the controls. 

"Sonic, look, the doctor is mutilated too, I doubt he would let his own creation murder him!" Shadow says, using the opportunity to throw a Chaos Spear into the press Robotnik's inside. The room begins flashing red as the Hydraulic presses begin falling and retracting at random. Sonic and Shadow quickly begin darting around the falling presses at high speed. 

"HOHOHOHO! Have fun, you miserable rodents!" Robotnik yells as he makes his escape. Sonic notices Robotnik getting away and begins charging up a Spin Dash. 

"Sonic, What are you doing!?" Shadow yells, but Sonic doesn't respond as he suddenly unleashes all the charged up Light Speed Energy at once, destroying all of the hydraulic presses in one swift motion. Sonic lands on the ground and motions for Shadow to follow him before he suddenly takes off. Shadow is caught completely off guard, but follows Sonic all the same. The Duo find themselves at the end of the room, the Doctor only just getting his Egg Mobile to turn on. 

"GET BACK HERE, EGGMAN!" Sonic yells as he spins through the Egg Mobile, causing it to crash back to the floor. Sonic suddenly grabs Eggman by the collar, "TALK!" 

"What's there to say, Sonic? You've already lost!" Robotnik says as a the entire base begins to shake and fall apart, "You see, I was just a distraction!" Shadow pulls Sonic off of Eggman and points a Chaos Spear at Eggman's head. 

"Distraction for WHAT!?" Shadow demands. 

"A distraction to give X enough time to power up, and I believe he got all the time he needed! You're too late, you horrible hedgehogs!" Robotnik answers as something flies by and grabs Eggman. 

"Metal Sonic!" Sonic yells as he rushes at the metallic copy of himself. Metal fires a barrage of Electric Orbs at the Hedgehog, knocking him back to the floor. Shadow throws a Chaos Spear at the machine, only for it to deploy the Black Shield to deflect the attack. 

"Sayonara..." Metal Sonic says coldly before flying off into the air. Sonic and Shadow look around for another way out, only for the base to erupt into flames. 

"Shads, I hope you have a way out of here...!" Sonic says, looking to Shadow, who quickly gets an idea. 

"Sonic, Charge up your Light Speed Attack!" Shadow orders, Sonic nodding as he begins charging up, soon glowing with a light blue aura. Shadow then extends his hand, Sonic looking confused. "Grab on, trust me!" Shadow orders, Sonic quickly grabbing the ultimate lifeform's hand. Shadow then suddenly throws the both of them off the ledge, activating his Air Shoes soon after. 

"Shadow! The explosions catching up!" Sonic yells out, Shadow not reacting. The fire begins to creep closer, the duo of Hedgehogs feeling the air around them heat up. 

"RELEASE THE ENERGY, NOW!" Shadow yells, Sonic letting all of the Light Speed Energy out at once, causing the duo to blast away from the flames and out of the Final Zone just before the entire place explodes into a pile of debris. The two hedgehogs are sent flying by the fallout of the explosion and land on a mountain peak. Sonic is the first one to get back on his feet, looking down at the burning remains of the Final Zone with an uncertain look. Shadow is soon to follow rising to his feet just in time to see a figure rise out of the flames. 

"Oh...Oh no..." Sonic says to himself as he balls his hands into fists, "ShadOW!?" Sonic yells back at Shadow, who quickly gets to his feet. 

"Here we go..." Shadow says to himself as X releases a massive blast of rainbow light, his screams of agony filling the ears of all those on Mobius. Sonic and Shadow avert their gaze until they feel themselves floating off the ground. 

"Woah, Shads, what's going on!?" Sonic asks frantically as he tries to grab onto something solid, but to no avail. Shadow tries to Chaos Snap away, but nothing happens, much to Shadow's horror. 

"This amount of Negative Energy...it's nullifying my Chaos Powers!" Shadow realizes in horror as he grabs Sonic and flies away as fast as he can, his Air Shoes becoming more unstable by the moment. 

"OH NO YOU DON'T!" X yells as he suddenly appears in front of Shadow, grabbing him by the neck as Mobius is enveloped in a deep purple haze. "I have had ENOUGH of foolish rats putting a stop to my conquest, you two will WATCH your world CRUMBLE!" X declares as Sonic and Shadow find themselves strung up by crimson chains. "Now then...let's put some of this energy to use!" X's body begins to morph, his body elongating and tearing itself apart the Negative Chaos Energy flows through it. X's shoulder snap as they begin to extend and elongate, ending at a sharp point. His arms and legs begin to become lankier, his skin tearing and ripping as a his shoes become longer, ending at sharp points at each toe. X's ears stretch and warp onto themselves, assuming a shape reminiscent to demonic horns. Finally, X's quills flare up, assuming a position similar to Sonic's own Super Form and a large X shaped cut forms at the base of his neck. The demon's body creaks and snaps as he moves his new limbs, taking in the new look with a sadistic smile. "How do you like the look? It really suits an emperor like myself." 

"We WILL stop you, X!" Sonic yells, yanking on the chains binding him. 

"X? No...not anymore...for the last moments of your pathetic lives...call me...Emperor X!" X retorts. X begins charging up Negative Chaos Energy, a deep purple aura surrounding him as he does so. 

"I don't get it, why do you want Mobius so much?" Shadow asks, yanking on the chains with as much force as he can manage. 

"Why? You actually think you two deserve an explanation?" X retorts with a laugh, before releasing all of the Chaos Energy at once, the blast tearing through the ground and quickly reaching the core of the planet. Sonic and Shadow look on in horror as the planet they've fought so hard to protect is detonated, reduced to cosmic rubble. The last thing they see before they loose consciousness is Emperor X laughing wildly, absorbing even more energy from the explosion.