A few months later.
Eggman came through the door to Shadow's private quarters. "General Shadow, meet your Commanding Officers." Shadow looked on as Project Alias had stepped through the door.
"Good... begin the attack!" A huge door was opened as the Omen Army marched onward towards their first destination, Angel City, the capitol of their beautiful land. There were more than two thousand soldiers marching into the soon to be headquarters of a new world order. Once all the Privates and Corporals were in the city, they stopped. Soon, the Officers came flying in above them. The attack began. Several buildings fell down in only a few seconds of the battle. One fourth of the city had already been taken in mere minutes. The National Guard only slowed their process. When their movement was halted, reinforcements had arrived, Project Alias. They flew twenty feet apart, at the same speed, at the same time. They both stopped, and looked at the battle, just as calm as a butterfly would on a flower. Then out of nowhere, they charged into battle. When they got within range, their identity was clear. They were, Metal Shadow, and Metal Sonic. It seemed like the army was doing nothing as Project Alias tore away at the city. Shadow was high in the clouds overlooking the entire city. Sonic and Knuckles were talking on top of a building. Sonic was trying to see through all the darkness.
"I can't see who it is, but he must be the cause of it all." Sonic was pointing up at Shadow, unaware of his identity. "Knuckles, throw me up there."
"Got it." Knuckles threw Sonic up into the air, where he transformed into Super Sonic. Shadow soon became visible.
"Shadow!" Shadow turned around towards Sonic.
"Sonic, so glad you could make it." Shadow was speaking in a sarcastic voice. Sonic couldn't believe his eyes.
"What are you doing!"
"I'm fulfilling my destiny, I am awakening Project Omen." Sonic wasn't satisfied with the reply.
"But why!"
"It is what I was created for." Sonic shook his head.
"No, I can't let you do this."
"Oh I'm well aware of that, which is why I've come prepared." Shadow pulled out the Master Emerald. "Project Alias, activate!" Metal Shadow and Metal Sonic soon came up and charged using the Master Emerald. They soon became Metal Hyper Shadow, and Metal Super Sonic. Sonic looked in awe. Shadow's eyes flickered red. "Attack this pathetic being!" The two Commanding Officers attacked Sonic, badly damaging him. He fell and landed next to Knuckles. "Forget Sonic, continue attacking the city!" Shadow watched and laughed as the helpless citizens cried for help. With non stop fighting, in one week, Shadow had control of the entire Mainland, and most all of the floating islands. General Shadow, was now, the ruler of all that still remains of his rampage, the Omen Army's rampage.
Forests were ordered to be burned, buildings were ordered destroyed, there was no place to hide. Sonic and the others stood no chance against all the chaos. Everyday marked an island's destruction. The only island that was spared, was Emerald Island, only because of its mysterious power. And so of course, that's where Sonic and the few survivors hid. Every now and then they'd get lucky and destroy a base, but where one fell, two appeared. There were no longer any beautiful plains to look at, no lush green trees, all desert, and wasteland; and General Shadow was proud of all of it. His robots and squads ravaged the land relentlessly. Not a day went by without death and destruction. Even after several years, tragedy always seemed to find Sonic and the few survivors.
It wasn't long before Sonic and Knuckles started retaliating. Shadow was walking through the forest of Emerald Island, when Knuckles glided in and knocked him down. Sonic too, soon came in to view. Shadow looked at them both. "So, you think you can take on me? You have no idea what's in store for you!" Knuckles stepped forward.
"Shut your trap and fight!" Shadow shook his head.
"As you wish." Shadow jumped up as Sonic soon followed. Shadow stopped and waited for Sonic to arrived, when he did, Shadow slammed him down to the ground. Knuckles suddenly jumped on a tree and began climbing it.
"That's it, I'm not gonna let you get away with this!" Shadow smiled.
"Alright, I'll give you a free shot." Knuckles climbed up and punched him. Shadow was surprised at the effect. But he quickly regained full strength, and landed. Sonic and Knuckles moved in on him slowly.
"You guys are pathetic; let me show you true power! Chaos Blast!" A gigantic blast came from Shadow and threw every thing back. Sonic and Knuckles were badly damaged, yet they stood up, pushing on the fight. Shadow sped towards Knuckles and uppercutted him, then jumped kicked him into several trees. Shadow landed facing Sonic.
"Shadow, you need to stop this nonsense now!" Shadow grappled him and kept him still.
"Nonsense? You think fulfilling my destiny is nonsense? No, what you speak of is nonsense!" Shadow increased his grip. "You don't know the half of what I've seen... I've seen the future, it is my hands! It is my destiny to avenge Dr. Gerald Robotnik!" Sonic gasped at this.
"What? Gerald Robot- you've got to be kidding me, he's dead!" Just then, Knuckles came in with a Power Punch, but missed and hit Sonic. Shadow then dropped Sonic and punched Knuckles, knocking him out. Shortly after Shadow became dizzy, and almost lost his balance. Sonic was still focused enough to see this. Shadow soon stood straight up, and turned to them.
"What... no, what's happening to me?" Sonic could barely speak.
"Shadow... help, us, please..." Shadow had a lost look on his face.
"I-I want to... but, I can't." Shadow stared at his fist, shaking, as he took out his emerald. "Here, this is all I can do." An energy beam came out of the emerald and into Sonic and Knuckles, healing them both. Shadow began to walk away when he turned his head to say one last thing. "Sonic... meet me, when the time is right, you'll know when, and where, don't worry, I have a plan." Shadow then continued on his way, as Sonic and Knuckles laid there resting.
Some time later
It had been a while since the day Shadow had become general of the Omen Army (No one knows exactly how many years it's been). Shadow was sitting in his quarters, thinking out loud. "I've taken control of the world... and I've got the only ones who refuse to obey me stuck into hiding... my task is almost complete... Colonel Eggman, come into my quarters." General Shadow was now speaking over the intercom.
"Yes General Shadow?" Shadow was fiddling with a map of the world.
"It has come to my attention that I no longer have any use for you." Eggman stepped forward in anger.
"I knew you'd try to pull something like this!" Shadow stopped looking at the map, and focused his attention on Eggman.
"Try? Oh, no, I AM pulling something like this. You see, I used you, and I won. You, are weak, and I, am strong. You lose."
"No Shadow, it is you that loses." Eggman pulled out a switch and pressed it. "Project Alias is now under new management!" Shadow stood up.
"What!" Eggman smiled.
"You put me in control of building them, and I installed a switch that allowed me to take complete control over them anytime I want. And right now seems like a pretty good time to me, doesn't it to you?" Metal Hyper Shadow and Metal Super Sonic came in. "Now then, DESTROY SHADOW!"
"Chaos Control!" Shadow was gone in a flash. Eggman chuckled.
"Hmph, calls me weak, then flees at the sight of trouble, pathetic." Eggman called in a conference and announced his promotion to general.
"I must begin quickly, he has acted much sooner than expected." Shadow was now at a secret base, that only he and a small separate army knew of. He began walking down a hallway, soon he too was in a conference room. "Listen up, the time has come to fully activate Project Omen, Eggman has finally made his move. You know what to do." Everyone began leaving the conference room, and entering a huge hanger. In it, was an enormous shuttle, and on the shuttle was the name, ARK II. As it began to activate, the army made haste for its entrance. When everyone was on board, it took off. As it flew over the sea and land, lasers and chaos drives were being fired in every direction, what was now Eggman's army stood no chance against the newly constructed ARK II. Shadow eventually flew it over Eggman's base. "Fire the Chaos Cannon!" A small cannon slowly made its way out of the center of ARK II. When it had fully emerged, it fired a beam twelve times the cannon's size. The base was obliterated. However, a figure that looked like Eggman and Project Alias had escaped. They landed about a mile from the site. Shadow left the ARK II for a final showdown with escapers. Eggman called out with much haste.