Ok so this is my first GI Joe fic. Snake Eyes/Storm Shadow pairing mainly, Duke/Cobra Commander on the side. Maybe a few more depending on where this one goes. Reviews inspire me~

All Characters in GI Joe belong to Hasbro. Cheap bastards.

Caught by a Cobra

It was over. The Joes had lost the war against Cobra and their base was taken over by the end of the first day. Most of the troops had been captured, and some had been scattered to the winds. Snake Eyes was one of the few that hadn't been caught yet, but living on the run was certainly no fun for the black clad ninja. The last few months had been sheer hell, running from cave to cave in the higher mountains of the Rockies. He had to keep moving though, never staying in the same cave for more than a night. The lower mountains were crawling with Cobra operatives, and even setting a foot outside of the caves during daylight hours was going to get him captured just like the others.

Snake Eyes had been listening into the conversations from Cobra's radio frequencies since he spliced into their system on that dreadful day. He had to admit, years of training with various Joes made him extremely knowledgeable about everything- from cooking with Roadblock to technological advancements with Dial Tone. He missed them all right now, they'd become a second family to him since the deaths of his own family before he returned home from the war… the only person that was missing from his new family was his sword brother. Without him, it wouldn't be complete, and Snake Eyes had planned to try to get him to come with the Joes eventually. The plan just never had time to pan out when they were fighting on the battlefield rather than talking.

Scarlett had been captured about 3 weeks ago, in a hotel in San Diego. They managed to corner her in her room and overtake her with numbers. Snake Eyes had told her to go her own way after they escaped from the base, mostly for tactical reasons. And the fact that he was having some issues with having her around…he was thinking more of a certain white clad ninja from the Arashikage clan when they were together, and rarely thinking of her in between their kisses and brushes. Hell, he could barely keep her in his mind while pressing her into the bed… and the fact that he couldn't complete the act without thinking about Tommy was bothering him. He wouldn't admit it to anyone, in fear that he might lose a friend and a lover if Scarlett knew… and if Tommy found out, he'd never speak to his sword brother again. It was too shameful to even think about it…

Roadblock was captured four and a half weeks ago, in a museum in Washington D.C.; where Destro had taken him down in a hand to hand combat scenario.

Tunnel Rat was caught in the first week, beneath the Joe's 'former' base. He was trying to find a way to take the base back by force and keeping the Joe's files safe. He ended up destroying them before he was captured, which made Cobra's search that much harder.

Falcon had been caught on the day they were taken over, fighting to the end with Hawk, Duke, Flint, Lady Jaye, and the others. Last Snake Eyes heard about them, they were being treated like prisoners of war… save for Duke.

Duke was said to be held by Cobra Commander himself. No one had said anything about him over the radio frequencies… and the last time he'd heard anything about him was the day they were captured. Cobra Commander was chuckling to himself about Duke's capture, holding the former commander's chin in his hand to force him to look at the blue clad commander's grey steel mask while Snake Eyes watched from above the conference room in the ventilation system. Tommy had thankfully not come along on this raid… though Snake Eyes knew why. The injury he'd given them in their last fight was serious, and even with immediate medical attention, there was no way that the white clad ninja would be active for a few weeks. The slash that Snake Eyes had made in his sword brother's arm managed to cut through four necessary muscle groups that controlled the basic movements of the arm. It hurt like hell to receive the injury, and if not treated within twenty four hours, it could result in the loss of the arm all together. Tommy managed to get back to base in five hours time, and their medics saved his arm, but landed him on restricted movement until further notice. Snake Eyes only fear was that Tommy healed quickly, and was on the prowl by now.

Cobra Commander had taken Duke as his own prize, keeping him chained up beside his new throne… the president's office. When Cobra had eliminated the Joes, they had no one to stand in their way of taking over the US government, and within a week the entire North American Continent had been conquered. Within the next 2 weeks, they conquered Europe and Africa… then Asia in the next week. Australia and South America came next, falling in less than five days with divided forces from Cobra. Cobra met with no resistance once they had control of the United States- including all of its weaponry, resources, and political influence. They ravaged the countries that once stood as their own homelands, and declared themselves the rulers. If radio records showed true, Destro and the Baroness had taken Europe as theirs, naming themselves the new king and queen of the entire continent. Zartan and his forces took Australia, Africa and South America, mostly for the terrain. Storm Shadow had been given all of Asia, and a nice little citadel on each continent to begin training new forces for Cobra Commander's standing army of enforcers. Cobra Commander has taken his role as Emperor of the World… and Snake Eyes was one of the only three targets left on his list to capture.

Other than him, the only ones left were Spirit and Kamakura. Spirit was away on a small mission in his native tribe's lands at the time of the invasion, and had remained there. Kamakura was taking a few days of to heal from his injuries from the recent battles, and was staying with his family while he was on Oxycodon for the minor surgical incisions that resulted from endoscopic surgeries. He's managed to get his ribs busted up and one of them nicked his pancreas, which caused it to leak fluids slowly into his lower chest and upper stomach area. He noticed the pain as soon as he returned from the mission, and Doc had treated him within two hours, preventing any real organ damage. Snake Eyes sent both a message saying to keep their heads low until further notice. They were safe where they were right now. Kamakura was young, there was no need to place him in danger, and Spirit had a good life where he was, why drag him into a fray when he could stay safe?

And speaking of necessary small surgeries, Snake Eyes was sure his old injuries were catching up to him. He had a slowly increasing pain in his lower right side. The pain had not relented as he tried to sleep the night before, and he began to toss and turn on his cave floor, covered in only a few blankets on the hard ground hidden behind the rocks with the moonlight flooding in behind him. The rocks gave him good coverage in this outcrop, covering him as he slept, but to anyone who entered the cave while he rested, it just looked like a large boulder was there. And since he'd doused the fire a few hours beforehand, no one could see the light from it. It was rather cold this time of year, but then again, he'd been out in the mountains for about 4 months now. It had to be October by now, if not November. Hard to tell when the changing trees were the same green pine up here, slowly being covered by the previous night's snow. It wouldn't be long until he had to find another source of warmth than Timber's head on his lap. The wolf had followed him this far, chances were he'd continue to follow him until he went back to the city. Then again… maybe it would be smarter to stay out here. With his injuries from the helicopter crash, he wasn't too sure if returning to regular society would be an easy transition of a military ninja…

After all, one couldn't wear a mask in an office building and not grab attention, or try to teach children the way of the martial artist when the parents never saw his face. But staying up here… in the peaceful mountains… away from everyone who would judge him… with his best friend, Timber… living off the land and relaxing whenever he wanted… catching his own food, getting his own wood for fire… it seemed so easy; all he really had to do was build a new cabin. Perhaps dig out a huge pit and cover it while he worked. Then build a small covered opening and bury the rest, to conserve heat in the winter and keep his head low until Cobra stopped looking for him…

A jolt of pain ripped through his stomach as he moved again. The aliment was getting worse. Darkness was turning to daylight, and Timber awoke when his master gripped his side in pain. He whined as he looked at his master with big puppy eyes. He knew something was wrong, but he had no idea how to make his master feel better.

Snake Eyes relaxed his muscles as he tried to ease his own pain with mental control. He looked at the young wolf's deep orange eyes and smiled at him, resting his free hand on the wolf's head and stroking it ever so gently. He started to get up to head down to the river and catch their breakfast. Not much was swimming these days, but it was easier to avoid guards in the middle of the dawn hours than after the sun had completely risen. After that, they could see the ninja's black armor in any light until sunset. He had to catch as much food as possible in this hour, and then make it back up to Timber and his belongings before he was caught.

Snake Eyes rose to his feet and started to run down the hill, slipping between the darkened shadows of the first minutes of dawn and the trees lower branches. He saw that a few had been cut by a large knife or sword… no… Storm Shadow wouldn't be here. He was still injured… he couldn't have healed that quickly.

Snake Eyes pressed forward and dodged a few more trees on his freefall down towards the river. He was forced to stop for a few minutes as he staved off the pain by focusing on his memories, trying to get some positive emotions running through his mind instead of pain. He managed to get up again, and finished walking the few meters to the river to catch his breakfast and hopefully lunch.

After about 40 minutes, Snake Eyes had caught his and Timber's breakfast. Two large fish. He couldn't remember what type specifically, but they were good enough. He was hoping the dawn would be more forgiving, but he had to run as his darkness was turning into light. He had to find some vegetables if he was going to eat lunch at all. He ran back towards his cave, grabbing a few leafy grape vines and some potato plants, figuring he'd just wash them back at the cave in the small trickle that came from the cave ceiling in the back. It was strong and pure enough to clean his vegetables. He would bath at night in the stream down below instead of trying to bath in the trickle that was only as big as his hand. Thanks to its smaller size, the water never let off that much noise, so it didn't give his position away.

When he arrived back at his cave, he saw two blue clad soldiers walking towards his previous position near the river. He couldn't help but feel a twinge of fear if they caught him here. He was still in a lot of pain, and trying to take on fully armed, battle ready Cobra soldiers was a very bad idea. Chances are that if he even moved near them, they'd take him out in a heartbeat- mostly due to the fact that he couldn't run quickly with the pain in his side.

Snake Eyes walked to the back wall of the cave, hidden behind the stalagmites and stalactites that added perfect coverage for him while he stayed here. He sat against the back wall and placed his food items to the side, resting the two fish on the grape vine leaves to keep them off the ground while he built up a small fire. As the fish cooked a few minutes later over the subtle flames, he started to wonder where his life was going. He was in a military specialized force… and they had been defeated. He was in love, but he felt nothing for the woman he was suppose to be in love with. He was a ninja without a clan… so what was he suppose to do with his life?

His thoughts were interrupted as he heard footfalls outside of the cave. He extinguished the fire with some dirt from the floor of the cave and pressed his body against the rocks behind him, grabbing Timber and holding his mouth shut to keep him quiet. The last thing he needed right now was to have his loyal wolf give away his position. Timber tried to whine for a second, only to have Snake Eyes glance at him silence the low winded sound. The footsteps got closer slowly, each one echoing off of the cave walls, threatening him as they came nearer to his position. He held his breathe, praying not to be found, and then heard a familiar, oddly calming voice.

"There's no one in the cave. Return to the camp site, I'll keep searching for anything in this one…" the voice growled. That melodious voice could only belong to one man… Tommy was here… his injuries had healed sooner than Snake Eyes expected. He was now dealing with a ninja who was trained by his clan… and frankly was a little bit better than him in most of the subjects. Tommy knew how to track, and even in this cave, covered by a stone floor, the chances of him getting out without Tommy finding him were next to none.

Snake Eyes heard footsteps approaching him, steady and strong. The closer they got the more Snake Eyes thought about running… he could sprint, jump out of the cave and try to fight off Storm Shadow himself… or he could stay put and pray that he wasn't found.

As the footsteps got closer to him, he held his breath. He didn't know what to do…

Step… step…step…stop.

And then the footsteps moved away. Tommy must have been less than 3 feet from Timber and him… and he didn't see them! Oh thank the heavens that he wasn't found.

Snake Eyes took a moment to catch his breath, relaxing his muscles from the stress of a near miss.

It was almost nightfall as Snake Eyes stood up and gathered himself. Timber started to walk towards the cave mouth, clearly needing to use the forest floor or a nearby tree. Snake Eyes stretched and followed closely after. Holding his water for that long had been tense, and he was still human. Time up here passed a lot faster in the winter months, and his pain made it seem that much more fast when he was trying to focus on something else. It must have been well past dinner time at the Joes regular schedule by now. The sun was setting and there were only a few more minutes to go until he could wander the forest freely to find dinner and get a little exercise. The sunsets up here were gorgeous… but he missed the old fashioned dinners in the Pit, the spaghetti nights and feared burrito dinners. He missed Scarlett a little... Duke more… and he feared for his students the most. He loved them like children… and he'd always liked the idea of having a family of his own. Too bad that looked so far away now. Chances were Storm Shadow would find him, and he'd be taken to prison soon enough… or turned into Storm Shadow's personal jester… or perhaps target practice…

Timber was already leading the way when Snake Eyes followed him. He walked down the darkened pathways formed by deer, moose, and wolves over the years. Not many bears up here thankfully, either that or they were all hibernating.

Snake Eyes felt a sudden sharp pain in his side and gripped it hard as he tried not to fall down. He stopped, grabbing the side of the mountain cliff and holding on tightly, trying to will it away.

"You know… it's pretty clear when you have a serious medical condition. Perhaps you shouldn't fight it this time and let us take care of you…" A cold, deep voice said from behind him. It was an unmistakable voice too. Tommy…

Snake Eyes whipped his head around as quickly as he could and looked at the white clad man. Storm Shadow approached him slowly. All the weapons stayed in their holsters… and Timber was nowhere to be found. Snake Eye kept his crouched position, gripping his side with all his strength. Storm Shadow stopped only a foot from him and kneeled. He reached out to gently pull the stubborn hands away from the other man's side, looking at the spot for any indication of what was ailing his sword brother. All he saw was the same toned muscular body that he'd trained with for so many years rippling under his touch. No sign of bites, scratches or human weaponry damage. It had to be something internal.

"Let me see… did you eat something you weren't suppose to ingest? Or did you just start feeling this pain?" Storm Shadow asked, gently running his fingertips over the black clad man's injured area. Snake Eyes only glared at him, and started to reach for his swords as stiffly as he could. Storm Shadow grabbed the younger man's wrist and pulled him into a hug, which earned a pained motion from the voiceless man. Storm Shadow actually felt bad about the pained expression, but held Snake Eyes close while removing his swords.

"Relax brother… you are in a lot of pain… and judging from the area of your pain… I'd say it's something serious. Let us take you back home and get you fixed up…I won't lose you to this when it can be fixed." Storm Shadow said while throwing the black colored swords over his own shoulder, and gathering up the struggling man into his arms.

"Don't fight it, you'll only end up hurting yourself more… and we can finish this arrangement when you are better. I won't hunt an injured man at an unfair disadvantage. That's not good sportsmanship…" Storm Shadow said as several Cobra guards came up behind them. Storm Shadow really didn't want to interact with the blue clad men right now, Snake Eyes was his only concern. But then again, he could get them to tie up the loose ends here while he attended to his lo- brother. Brother.

"Your orders sir?" One of them said. Storm Shadow turned to them, holding the black clad, pain stricken man tightly in his arms like a child would their favorite and most beloved toy.

"Get his belongings, they are in that cave. Also tranquilize the wolf and bring him with us. Don't hurt him. I want the wolf alive and well." Snake Eyes barely heard the white clad man's orders as he was carried to one of the two nearby transports and carefully laid on a gurney. Before he could register what was going on, he felt a needle insert itself into his arm and the pain medication fill his systems, overtaking his mind in a haze of foggy surrender. The last thing he remembered was a warm blanket coming over his body and Storm Shadow looking down at him while covering him.

"Relax brother… you're safe for now…" Storm Shadow said, running his hand down the black clad man's cheek gently as he watched his sword brother's eyes droop from the medications. The transport began to take off as Storm Shadow sat down in the seat that would normally be occupied with a medic checking the vitals of injured soldiers, holding Snake Eyes unconscious hand in his own. He'd already lost his clan… he didn't want to lose his sword brother too. He could only think of the fond memories that entertained him while he was in Cobra as the transport headed back to the castle in hi new domain… and old stomping grounds.


And fin~

Ok, read, review, you know what to do~

And all criticism is taken constructively (as long as it's not intentionally abusive).