Hey there! This is my first fan fiction I'm writing for this site. I came up with this idea today: basically, it's the story of Sonic Adventure 2 mixed with Pokemon. I'm using the way Sonic X did this for inspiration. Also, there's going to be some Advanceshipping in this story; just thought I'd let ya know.

Note: rootedinjesus does not own Pokemon or Sonic, but you knew that already.

All right! Enjoy! Feel free to rate and review!

Chapter 0: Awakening

An alarm blared loudly as the musty old factory bustled with excitement. The people who worked there hadn't seen any excitement like this in a long time, as they'd long been retired to work behind the scenes of their organization rather than on the front lines. Today, however, they'd have to do a throwback to their glory days before everything went downhill thanks to one meddlesome kid.

"WARNING," blared the alarm. "LEVEL 1 SECURITY DOOR BREACH. ALL TEAM ROCKET AGENTS, TAKE UP YOUR OLD POSITIONS. REPEAT: ALL TEAM ROCKET AGENTS, TAKE UP YOUR POSITIONS. THIS IS NOT A DRILL. ROCKET FACTORY N IS UNDER ATTACK."

None of the Rocket agents knew who was invading them, or why they were being invaded in the first place. This facility had largely been forgotten by the world, or so they had thought. They'd always been told to stay sharp in case of something like this, but the years of boredom behind the scenes had rusted them so that they were like the factory: dull and forgotten. But now some of them cursed themselves for not being sharper than that.

While they got themselves ready to take on the intruder, he, meanwhile, cackled to himself. "This is too easy! What thick-headed fool built this system in the first place?! Ha! Maybe I can negotiate a deal with ol' Giovanni for better security...unless, of course, this is his preference."

The intruder was a large man whose body had an abnormal egg shape to it: he wore a red blazer, white gloves, and black tights. His eyes were hidden by two monocles, and his bald head adorned a metallic device that made him smarter. He had a thick, ginger mustache under his pink nose. His name was Dr. Ivo Robotnik, or at least it had been. Recently, he'd decided to take on the alias of Dr. Eggman, but that's largely irrelevant.

He had no trouble plowing through the defenses, since all of the Rocket agents were too out of touch with their old skills to do anything noteworthy. Soon, he reached the object of his excursion: a chamber sealed away and forgotten, just like the factory.

"So this is Team Rocket's top secret ultimate weapon, is it?" he sneered. "It looks a lot smaller than I would've expected. No matter; there's no reason it's not powerful if it's under this much security. They probably weren't expecting anyone to know how to unlock its powers. Good thing I'm about to prove them wrong!" He then went up to a keyboard and looked up at a hologram screen that had the word "PASSWORD" written across it. He smiled and typed in, speaking as he did so, "MA-RI-A. Maria! There! Now let's see what this sucker can do," he finished, pressing Enter. Steam billowed out of the machine as the cylindrical canister fell away. As Eggman looked on, he noticed a familiar shape emerge: spikes on the back of his head, long legs suited for running, and a muzzle underneath two eyes.

"Oho!" he raised an eyebrow. "I should have known you'd try to stop me. You never fail to surprise me. And here I thought I'd finally gotten away with something without you noticing!" But when the steam cleared away, he got a better look at his companion who, as it turned out, was black and red, his front sporting a tuft of white fur, his eyes a cold red, and his mouth, in stark contrast to what the mad scientist was used to seeing, was frowning. "Wait a minute," he breathed. "You're not Sonic! How...how can this be?!"

The black hedgehog spoke: "My name is Shadow. I am the world's ultimate life form. Since you were so kind to awaken me, my master, I will be so kind as to grant you a wish."

Master? Eggman thought gleefully. This is not what I was expecting, but I like it!

"Hold it right there!"

The two turned to see two Rocket agents standing in the way of their exit. "Did you really think you could get away that easily, Doctor?" one of them, a boy, jeered.

"Well, I was expecting a fight, but I think I'll skip out this time, Brat," Eggman smirked, turning to Shadow.

"My name is BUTCH you dingbat!" the agent snarled.

"Let's just get this over with," his female companion, Cassidy, reached for her belt and fished out a Pokeball. "Go, Golbat! Use Air Cutter!" She threw the Pokeball out, and it opened, releasing energy that materialized into a blue bat-like creature.

"Golbat!" it screeched, folding in its wings and charging at Eggman's pod-walker. It hit dead on, short circuiting his machine.

"Blast it!" he cursed. "I knew I should've gotten that warranty!"

"Leave this to me."

"Hm?" everyone turned towards the black hedgehog, who stepped forward with a clenched fist and a menacing glare.

"If you value your life," he snapped, "recall him. Otherwise, you'll face the consequences."

"Team Rocket never cared about consequences," Cassidy snapped. "Golbat! Use Air Cutter on this weapon!"

"Bat!" the Golbat shrieked, charging at Shadow. He jumped to the side, letting Golbat crash into the wall.

"Guh! Try again!" Cassidy yelled. Golbat obeyed, but was met with the same result. "Again!" Cassidy called, and the situation repeated itself until Golbat fainted from exhaustion. Cassidy recalled it.

"Let me handle this," Butch snapped, throwing out his own Pokeball and releasing a large, steel snake-like Pokemon. "Steelix! Use Bind!" Steelix obeyed, wrapping Shadow up in its metal body and squeezing the life out of him. "You see? All you need is a little power, and –" Butch didn't get to finish gloating, as a sudden blast of power knocked Steelix off of Shadow and onto the Rocket agents. Shadow stood there, unharmed.

"Get out of my sight!" he snarled. Butch recalled Steelix and the two Rocket agents dashed out, shouting the retreat. "Hmph! Pathetic humans," Shadow muttered under his breath so that Eggman couldn't hear.

"That was brilliant, Shadow!" Eggman cheered, elated at his newfound ally's power. "You really are as powerful as my grandfather predicted." Shadow lowered his head on hearing this. "But what did you mean when you would grant me a wish?"

Shadow turned and looked at him, a strange aura in his eyes. "All will be revealed in time, doctor. For now, I must part ways with you." His hover shoes glowed brightly, and he lifted up into the air.

Eggman looked confused. "Wait, what?! Where are you –"

"I'll be waiting for you," he turned back and looked at him, a strange smile on his face, "on the Space Colony ARK." Then he disappeared.

"The ARK?" Eggman wondered. "Whatever could he want me to see there?"