Disclaimer: I don't own the Sonic franchise. Sega does.

Authors Note:

I realize I have not updated this in a very long time, but I found some chapters I had written for this sotry and never got around to transfering from paper to computer. I will see if I can finish this story, but I will not garuntee anything. Hope all of you who wanted me to post another chapter enjoy this one.

Chaos

Chapter 3

Shadow woke to a dark silence, his head pounding from unknown causes. Slowly, he got up and tried to assess his current location. He was in someone's room apparently, and from the looks of it he could guess where he was. Suddenly all his memories came rushing back to him, the clones, the emerald….and Rouge. On remembering Rouge, Shadow quickly jumped from the bed and rushed from the room. His sudden exit startling Sonic, who was sitting on the couch facing both the doorway Shadow emerged from and the TV he had been watching.

"Shadow? I didn't think you would be good for another few days…"

Shadow eyed Sonic for a moment before making his smirked response.

"Hmph…I've seen worse. Where is Rouge? She ok?"

Sonic pointed to a door down the hall.

"Your girlfriend is in the basement, down the hall and to the left. She fell asleep on your bed you know, real worried about you. We placed her in the basement bedroom when we got back yesterday."

Sonic's answer had also been meant to irritate Shadow, but he paid little heed to it and moved towards the door Sonic had indicated. The basement-converted-bedroom still retained many aspects of what it was prior; the only real changes being that there were no water pipes or anything similar in plain sight. The room only contained a cabinet/dresser, a few boxes, and the bed Rouge was currently sleeping on. The basement was also divided into two parts, a wall blocked off access to the rest of the basement, the only visible access point being a large, sophisticated looking metal door with a card slot next to it. Shadow sat on a box near Rouge's bed and started thinking. He found himself not only worried about Rouge, but what he, no, all of them, were going to do about the new threat Eggman had unleashed.

Rouge stirred slightly, snapping Shadow from his thoughts, and shifted them back to the white bat he was sitting close to. Even though Shadow had always known on the inside that he cared for Rouge more than he let on, it took the event that had recently taken place to finally allow his mind to accept it. And now that it had, Shadow found himself in a position that was unlike anything he had ever faced before and remained unsure as to what to do about it.

The white bat in question began to stretch and soon rose with a yawn. Shadow panicked for a second, he hadn't really thought about her waking so soon, even if he didn't know how long she had been asleep. He also didn't really know why he was down here; he felt he needed a better reason than "just because." Rouge didn't immediately notice him, probably still trying to fully waken, so he decided to go ahead and say something before she did and he looked foolish for just sitting there staring at her.

"Hey, feeling ok?"

Rouge gasped slightly, startled, and quickly turned to face him. She probably hadn't expected someone to be watching her sleeping, least of all him.

"Shadow? I'm fine…Why are you up? You're still hurt!"

Shadow hadn't really thought about his personal condition until Rouge mentioned it, only now noticing the amount of bandages on him, some coated him a light reddish tint.

"I'm fine, just a few scrapes. I've seen worse."

Rouge frowned, obviously not satisfied with his answer.

"If that's a scrape I would hate to see a cut…Well, why don't you let Tails take a look at you? Come on."

Rouge got up from her bed and began to exit the basement, pulling Shadow along with her. The pair walked into the room where Sonic was still watching TV.

"Hey Rouge, see Shadow got you up."

Sonic chuckled after the last few words. Rouge didn't pay him any mind though.

"Funny blue-boy, just cause you don't have Amy around is no reason for you to poke fun."

Sonic cleared his throat and continued watching TV, his fun killed. Amy had finally matured in personality and didn't pester Sonic quite as much, and with her annoying antics finally dying out Sonic was able to see some of her finer qualities. The two had finally become an item of sorts not that long ago, but Amy had gone to visit some family for a couple of weeks in a city on the opposite coast, Felucia. Now that Sonic was subdued some Rouge decided to question him on Tails whereabouts. The fox was always busy with something.

"Have you seen Tails? Since Shadow is up he might as well see how the wounds are."

Shadow frowned.

"Rouge, I told you I'll be fine."

Rouge took another look at Shadow to see how truthful his words spoke. The only real thing that seemed wrong was the bit of crimson on some of his bandages, but that could be enough in the proper environment, Ultimate Lifeform or not.

"Well, at least let Tails take a look. You want to be in top condition the next time we see Eggman don't you?"

Shadow took on a bit more serious expression at the mention of the evil doctor's name, but made no further arguments. Besides, he felt like he had to because she asked him, but didn't know quite why. Sonic came alive at the mention of Eggman's name, remembering now some information he wanted to share.

"Me and Tails went over to where you said that base was at to get a good look at it. The entire place seems to be dead quiet. Eggman's up to something, I can feel it. I wanted to check it out more, but Tails said that it wouldn't be a good idea cause of those damn copies so…"

Tails came into the room just as Tails began to trail off.

"Hey Sonic, is Sha…Oh, good, everyone is here. Take it your feeling better Shadow?"

Shadow only nodded, not really feeling in the mood to talk. Rouge on the other hand had no such feelings.

"He says he is, but can you see? You are the resident medical expert."

Tails perked up.

"Sure, while I take a look at Shadow I have something I would like to tell you all. This way."

The group followed the orange kitsune into his normal lab where he began to unwrap Shadow's bandages as he spoke.

"I figured out a way were we can tell each other apart from our clones. Eggman will probably use the fact that they are practically indistinguishable from us to frame us or start fights amongst ourselves, lowering our trust in each other."

Tails finished the unwrapping and proceeded to look at Shadow's wounds, but found that they had all completely healed up. There was no sign of his previous injuries, something that Tails found utterly amazing, healing that fast was overnight was amazing. He would have to see just how Shadow's healing abilities worked when this was over…

"Seems Shadow has completely healed, all his wounds are gone."

Shadow tossed any remaining bandages into the trash bin and smirked.

"See? Just a scrap."

Rouge thought that Shadow was being too arrogant, but decided to stay quiet so the kitsune would finish with what he had been saying. Tails, who was now finished with attending to Shadow, just sighed and walked over to a computer console and began typing out some commands. The black hedgehog obviously had a bit a Sonic's overconfidence.

"Now, while we won't be able to prove anything the clones do as part of Eggman's agenda, we make it so that the clones can't just replace one of us to keep us from being able to trust one another."

A beep is heard a machine next to the computer Tails was using comes to life. A fine mist begins to emerge from it as the top rises, revealing 5 vials of an unknown, glowing blue substance. Tails picked up one of the vials and held it carefully, showing it to the labs occupants.

"It took me a bit, but I managed to make this serum of nanite's made to be injected directly into the bloodstream. Once in the blood it travels up to the brain and attaches itself to the area that controls your sensory organs, particularly the part that controls your vision. The serum will allow to "feel" anyone else who has the serum also injected into them. And, once fully established and configured to the functions of your individual brain patterns, will allow you to see a faint glow from them as well. It also has a small tracking device in it, so if anything were to happen to us we can be easily located from any device configured to the nanite's particular wavelength."

Shadow didn't really feel comfortable with the whole concept. He really didn't like being injected with anything, previous experiences all unwelcoming. But that wasn't the only reason.

"Wouldn't Eggman be able to detect them? Plus if you can track us then so can he."

Tails took no time in reassuring the group.

"While Eggman may normally be able to detect something like this, it's highly unlikely that he can detect these particular ones. I configured them so that they seem like ordinary proteins; thus they seem more like a natural biological function than nanite's. The frequency of the tracking device is super encrypted, so even if Eggman did notice it he would have a hard time breaking it, I made sure of that. It also has a failsafe to change frequency if that ever happens. Anyway though, Eggman never really looks for this kind of stuff anyway, he is usually only interested in Chaos wavelengths."

Shadow still had his doubts, but decided that he would go along with it anyway, who knows? Might end up being useful. Tails proceeded to administer the nanite serum to himself and the rest of the group. Once this was accomplished Sonic decided to let the group on his "plan of action."

"Alright, here's the deal. After checking out that base with Tails we went over to the Floating Island to update Knuckles on what was going on. We tried to get him to come back with us, but he wouldn't leave his stupid rock with Eggman active again, so we are gonna go over there to get him before we make our way to Eggman's base. He got a recent gash on his hand from some rock-climbing incident, so that's how we can probably tell him apart from any clone that could take his place. That was Tails idea. Anyways, once we hook up with Red we go and kick some ass!"

Rouge sighed; Sonic was always so direct. He was gonna get himself killed one day…Shadow too, but at least he wasn't quite as bad as the blue one.

"Don't you think that's a bit too direct?"

Sonic seemed to think for a moment. To Rouge it was more like blank staring.

"Yeah….well, it's more fun that way."

Sonic let out a big grin, which Rouge wanted to slap off him so bad.

"Fun?" She thought, "being chased by Eggman's war machines and risking my life needlessly is not my idea of fun."

Shadow and Tails seemed to be fine with Sonic's "plan," so she decided not to argue, there would be a time and a place for that.

A few minutes later the group was airborne, taking the Tornado II towards the Floating Island. Tails was piloting while Rouge sat in the co-pilots seat; Sonic and Shadow stood on opposing wings of the aircraft. Most of the way was silent, with the exception of Tails and Rouge occasionally striking up a conversation, but Shadow and Sonic remained silent the entire way. The wind drowned out almost all sound outside of the cockpits, so conversation with the two was not very practical anyway.

A few hours after the start of the trip the group entered the Floating Islands airspace where Tails brought the Tornado to a landing on the southern side of the island. An airstrip had been built there when Eggman had first managed to trick Knuckles into thinking Sonic was his enemy and gained control of the entire island. All the structures that Eggman had constructed here had long been demolished, but Tails had managed to convince Knuckles to leave the airstrip intact for occasions such as this. Once the group had disembarked, Tails hid the plane in its usual hiding place, a growth of thick trees near one end of the airstrip. With the plane hidden, they all began to move towards the center of island, near the mountain's base. This was were the shrine of the Master Emerald was located, and with it, Knuckles. As Shadow followed Sonic in zipping through the dense jungle, something which kept the pair from running at their full speed, Shadow took in some of the sights the island had to offer from ground level. As Tails, who had taken to the air with Rouge as a method of reaching the shrine, had flown over the island Shadow had taken the opportunity to notice several of its features. One thing he found interesting was that on the other side of the approaching mountain there lied a desert, the reason he found this so peculiar was that it was only a small portion directly behind the mountain. The rest of the desert was surrounded by thick jungle.

As Shadow continued to follow Sonic towards the shrine he tired to take note of many of the interesting flora and fauna he had never seen before, some seemingly very unique. Maybe he would come back here when they finished with Eggman. Shadow erupted from his thoughts as Sonic's voice filled his ears, notifying him that they were about the reach their destination. The two blurs burst from the jungle and came to a stop in a small clearing, the Master Emerald shrine being in it's center. Rouge and Tails landed momentarily afterwards, both looking kind of tired with trying to keep up with the two hasty hedgehogs, even if they were not going at top speed. Sonic ran up the stops of the shrine.

"Knuckles! Hey Knux! You here Red?"

A rustle to his left caught Sonic's attention as the echidna came out into the open.

"Sonic! Good to see you could make it, kinda soon though isn't it?"

Sonic motioned towards Shadow.

"Yeah, Shadow here healed up faster than we thought."

Shadow looked towards Sonic at the mention of his name. He had been transfixed on the Master Emerald, he felt as if something was pulling him towards it, calling out to him. Shadow normally only felt this when he had a Chaos Emerald in his possession and was near another emerald. But even then, it was never quite this strong. When Sonic had mentioned his name he decided to ignore the matter and concentrate on the more important matters at hand, the last thing he needed was a bunch of distractions. Knuckles had begun making his way to the top of the shrine in order to join Sonic near the Master Emerald.

"So, what's the plan again blue boy? I want to get this done and over with as soon as possible. Having my island or my emerald threatened isn't something I'm fond of."

Knuckles reached the top of the shrine and stood directly in front of Sonic. The blue hedgehog didn't know why, but he was actually feeling a bit intimidated by the way Knuckles was standing in front of him. Something was wrong. On looking down Sonic found out what it was, the echidna's hand was free from any marks. It was too late for him to make any reaction though; Knuckles had already noticed Sonic's hesitation and knew he was caught. Then, not being one to give up an opportunity, nailed Sonic with all his strength right in the stomach and chest area. Sonic, who hadn't had a chance to put his guard up, doubled over in pain, all the wind knocked out of him. As Sonic felt the impact from Knuckles blow he heard a few ribs crack from its force. A normal person would probably have a huge hole in their chest seeing as how Knuckles was able to destroy large boulders with one hand. Good thing he wasn't normal, but he wasn't invincible either and felt his vision start to blur. Knuckles wasn't done with the blue blur yet though, and decided to take him out while the opportunity was present. After his last blow he whirled around and gave Sonic a hard hit on the back of his neck as he fell towards the floor. It was enough to effective take Sonic out; he had lost consciousness before he even hit the floor.

The remaining three friends hadn't anticipated such a turn of events and couldn't react fast enough, but Shadow was the first to pull into gear. Just as pseudo Knuckles finished his elbow maneuver on Sonic, Shadow gave him a fierce upper cut that sent the offender flying into the air. The black hedgehog then tried his patented homing attack, but Knuckles wasn't stupid and had fought Sonic several times before, so he had grown well versed in dodging and blocking such attacks. Knuckles managed to dodge Shadow and landed on the ground not far from where he had.

"Shadow, wait! That Sonic was a clone, I can prove it!"

Shadow hesitated for a second, not sure whether to trust the echidna whom he had never really met, but then he noticed his hand. He had remembered what Sonic had said they were to use to identify if the echidna was real or not, and this one didn't have any identifying mark.

While Shadow had begun to engage Knuckles, Rouge and Tails ran over to assist Sonic in what ways they could. He was in pretty bad shape, but the kitsune knew it wouldn't be all that much of a problem to get his blue idle back into shape. Sonic had suffered worse than this. Rouge, who saw the look on Tails face, decided to look into Shadow's fight. She knew how Knuckles fought from their previous encounters so she knew several of his weaknesses, but she wondered whether or not she should interfere.

Shadow ran towards Knuckles, who managed to jump over him just in time to avoid the painful blow that was to be dealt him, but not enough to escape Shadow's abilities. As the red echidna flew over him Shadow did a 180, facing him directly, and stretched out his hand.

"Chaos Spear!"

Yellow blades of energy shot forth from Shadow's hands, engulfing Knuckles and biting deeply into his flesh. The attack was much more potent than Shadow had been expecting. As Knuckles fell Shadow ran towards him and executed a powerful kick that sent his victim flying towards the Master Emerald Shrine. Pseudo Knuckles had only been minutes into the fight and was already pretty beat up, cuts and bruises covering him. From the looks of it Shadow figured the echidna might be close to finished, but as he finished that though the clone stood up like nothing was wrong, and started laughing. It was only then that Shadow noted that the wounds he had were not bleeding like they normally would.

"What do you think? A gift from the good doctor, nanite's in my blood heal my wounds as they open and keep fatigue from getting to me. You have no chance."

Shadow smirked at the overconfident echidna.

"Fool, nanite's won't heal missing limbs."

Shadow dashed towards the echidna in an attempt to get behind him, but to his surprised the red clone moved fast enough to get out of the attempt. Shadow dashed towards the echidna once more but he again moved out of the way, a new vigor seeming to course through him. The echidna began speaking as he barely managed to dodge some of Shadow's offense.

"Did you know Shadow, that at this moment you and Sonic are destroying Station Square?"

Shadow's ears perked at this, but he concentrated more on causing the red impostor pain than on such information. Or at least he tried to. Knuckles, who Shadow noted was a bit faster, grinned evilly as he dodged the black and red hedgehogs next move.

"Do you know how many the both of you have probably killed by now? More than 12,000 I would say…"

Shadow knew something like that would probably have happened at one point or another, but the information given to him so plainly fed his already bursting anger.

"YOU BASTARD!"

Shadow felt his rage build up, then burst forth, giving him great amounts of energy for only but a moment.

"Chaos Control!"

Shadow appeared directly behind Knuckles and planted his hand directly into the red echidna's back.

"Chaos Spear!"

White-hot bolts of energy tore through Knuckles chest, blood gushing forth from the many wounds. Shadow turned and kicked Knuckles into the ground with enough force to make an outline of his body in the ground, then he landed next to Knuckles and picked him up by the neck and glared at him dangerously.

"Now…your going to tell me where Eggman is and what his plans are, and I had better be satisfied with your answers"

Knuckles seemed to struggle with his words for a minute before finally speaking.

"I…have only…one thing…to say to you…good bye."

Knuckles gave Shadow a blow that was hard enough for him to loosen the grip he had on the fake echidna so he could get free. Shadow immediately tried to re-secure his hold on the clone, but when the echidna hit the ground a while engulfed him, leaving no trace of his former presence. Shadow growled.

"Damn."

Rouge came over to Shadow now that he was done with the fight.

"He probably had one of Eggman's teleportation devices…Shadow, we should go, Sonic has a few cracked ribs caused by Knuckles punch and does need a bit of medical attention. Plus we still need to figure out what to do next and what happened to the original Knuckles."

Shadow nodded and walked with Rouge to where Tails had been doing what he was able to for Sonic.

"Shadow, can you and Rouge help me carry Sonic? Knuckles, the original one anyway, has a place at the mountains base that has most of the supplies I need to fix Sonic up with."

The group had to be careful when they picked up the blue hedgehog, not wanting to cause him any more injuries than he currently had. The area Tails brought them to wasn't very far from the shrine. It was a cave carved into the side of Death Mountains base, and from its looks it was fairly obvious that it was man-made so to speak. The deep scratches in some walls and the unnatural smoothness on others was evidence enough. Also in addition to that was the lack of anything you would normally find in naturally formed caverns, like stalagmites and such. The entrance to cavern was more or less the size of regular door that opened up to a fair sized chamber branching of in different directions, each leading to different rooms. Tails had the pair place Sonic in one of the adjacent rooms while we went to find what medical supplies he could. On his return he began to treat Sonic for what he could.

"We are going to have to stay here for a while. I'm sure it goes without saying but I heard everything that clone said. And, knowing the military, the first place they will probably look for us is at my workshop. Later on I am going to have to return there though, there is some equipment there I will need as well as the Chaos Emerald Shadow brought back with him."

Shadow had almost forgotten about the emerald, and now that he did remember he wished he had it with him. It would have given him a nice boost for what he was about to go do…he might have to go for it anyway, he really did need that boost.

"You and Rouge stay here then, I'm going to pay myself a visit."

Rouge already knew what Shadow was thinking of.

"Shadow! No! Remember what happened last time? What makes you think you can just take them out now?"

Shadow had already started to leave, his mind set.

"Last time we were in a Chaos proof room, this time I wont be. Not to mention I'll have a Chaos Emerald as well, that gives me an advantage. Tails, where is the emerald anyway? I'm usually able to sense Chaos energy and I never sensed the one at your workshop."

Tails grinned before answering.

"Yeah…Eggman has always been very persistent with trying to find the emeralds, so I made a type of jammer that blocks off Chaos wavelengths. Its made almost in the same manner that Chaos resistant metals are, but its not nearly as hard or expensive. It's light too, I have one on the Tornado II as well."

Shadow sighed.

"That's great Tails, but not quiet what I was asking."

Tails blushed slightly, realizing he got carried away.

"Sorry…the basement under the shop is divided into two parts, the room beyond the metal door has a safe hidden underground. You will have to look for the button to raise it, its hidden on the wall right of where you will enter. Here is the passkey for the door. The safe has two emeralds by the way, yours and one me and Sonic had found some time ago."

Shadow pocketed the key Tails gave him. Two emeralds…he liked that, they would boost his power a fair amount…but three…

"Tails, your plane can fly without the use of its Chaos Emerald right?"

Tails eyed Shadow a moment, he knew what the black hedgehog was thinking and didn't particularly like it. Shadow wanted to take the Tornado's emerald, but know was no time to be selfish or untrusting, so he decided to go along with him.

"Yeah…it has fuel cells that are charged with power in case anything ever happens to the emerald. You can take it, but don't lose it."

Shadow nodded.

"Great, thanks."

As he started to leave Rouge blocked his way by putting a hand on his chest.

"Hey...don't go and do something stupid, ok?"

Rouge let Shadow go and gave him a quick peck on the lips before walking off. Shadow found himself very much surprised and at a loss for words, so merely nodding he continued on his way. He tried not to let himself thinking about it anymore than necessary, so trying his best he pushed the event into the back of his mind and blasted off full speed towards the Tornado. Now that he knew the way he was able to cover the ground in seconds, reaching the plane much faster than when they had left it. Shadow walked over to where the Chaos emerald had been stored, only to find it missing.

"Shit!" Shadow exclaimed and hit the side of the plane, denting it slightly. Three emeralds would have given him a good advantage, but now he could only hope that the other two emeralds in Tails workshop had not also been taken. Shadow quickly performed Chaos Control and appeared at Tails' workshop in a flash of light. On entering Shadow found that everything was still as they had left it. If what Tails' said was true, then the military must still be engaged with his and Sonic's clones in Station Square. He entered the basement and used the key to gain entry to the walled off area. It was really messy, part from all kinds of different machines in the process of being constructed lay scattered about. There were two long tables on either side of the rooms walls. One of which sported a really high-tech looking computer, the other parts to some kind of machine Tails' was building and various schematics to accompany it. Shadow began searching along the wall for the button, eventually finding it hidden in a portion of false wall. As he hit the switch the hum of machinery could be heard as the center portion of the floor began to rise, reveling a large, black meta safe. Approaching the safe, Shadow found a card slot and inserted the key card Tails had given him. The safe granted him access, the hiss of the locks unengaging heard before the door opened. As it did Shadow could feel the combined power of the two emeralds lash out, calling to him. This feeling was rushed by his anticipation as he reached in to pull the emeralds out. As Shadow held the emeralds in his hand he could feel his power multiply. This, however, was not normal. As his mind got more used to this new vigor coursing through him, he was able to see just how abnormal this was. His body had become engulfed in green flames of Chaos energy, while the emeralds themselves where disintegrating and being absorbed by his body. Normally, this only happened when one used all seven gems to achieve a higher level of power. Whenever he held a Chaos Emerald before he had only been able to use a portion of its energy to call forth different Chaos attacks or amplify his natural ones. The more emeralds he had the more he could use the attacks and the more powerful they would become. But now with the Emeralds being absorbed into them, he could use all of their power. The Chaos fueled flames had died down by now as Shadow had completely finished taking in the essence of both Emerealds. For a moment Shadow wondered what he would do if he ever needed the emeralds back in their physical form, but decided not to worry about it just yet. Instead, he tried to sense the limits of his new power, finding it in likeliness to being in his super form, but watered down a bit. He noted that his muscles had tightened and gained a better tone to them, making him physically stronger than he was before. Shadow also noticed that his senses seemed sharpened, and they already been pretty sharp to begin with. He smiled at this new outcome, though part of him wondered why it never happened before, but he decided not to complain. Forming a picture of Station Square in his mind, he called on the power of Chaos Control once more and disappeared in a flash of light, leaving behind only a scorch mark to prove he had been there.