Summary: "You told him he would be unharmed." – oops. "Let's hope he doesn't put up much of a fight." – wrong again. What if things worked out a little differently in the end? A different take on The Storm/The Eye. Shepwhump

SPOILER ALERT: If you haven't seen The Storm and The Eye, well, get on it, and I wouldn't recommend reading this first, you'll be completely lost and I guess I ruin a few things.

Disclaimer: I own nothing, and I'm still upset about the cancellation and the most likely scrapped movie :(

Warning: This is a WIP, randomly started about 6 hours ago. I've got a week before I head to CO Springs for Air Force Academy Basic Training (living the dream, right!). So here is hoping that I can finish this up decently in my limited time frame. It will most likely not be finished, but I'll try my very hardest as this idea has been floating about my head for years.

Additional warning: Mild Language so far. Rating may go up, not sure exactly where this is going yet.

The Diverging Storm

Part 1/?

Major Sheppard was fuming. He'd given the guy a chance and of course this was his reward for that small amount of trust. Not that he had actually had an option. He decided to vent a little anger. Hell, there was little else he could do right now. "Let me tell you what you did wrong here, Kolya. A - you lost two of your men. B - you damaged the switch before I could separate the grounding rods, which I'm sure you're gonna get an earful from McKay for; and C - you lost all of what little credibility you had with me!" He'd said his piece and hoped for a quick response. The storm was fast approaching and the wind was stealing his breath away.

Dr. McKay obviously heard the disembodied voice of the soldier over the radio, and it was not good news. He turned to face the Genii commander. "Do you have any idea of how big a setback that is? I may not even be able to activate the shield. I mean, I can't possibly –" the Genii soldier responsible for his injury forcefully grabbed his bloodied arm to quiet him. Rodney reacted immediately, his voice tight with pain, "Get off me!"

Acastus Kolya glanced at the exchange with little interest, more focused on the loss of his men. His eyes rested momentarily on Dr. Weir while he pondered his next move. "You killed two of my men," he stated coldly.

"I guess we're even!" sounded the barely discernable, but very angry voice of Major Sheppard over the radio.

"I don't like even," Kolya replied as he stiffly removed his handgun from its holster at his side.

"I'm not finished yet!" The threat did little to intimidate the commander. The wind whipped the major's words away and his voice sounded small and unconvincing.

He had made up his mind. This was the perfect play. Sheppard obviously cared too much for the city and its occupants that fell under his protection. "Neither am I." The way to hurt a man like him was easy, too easy. "Say goodbye to Dr. Weir."

The horror and fear were tangible in the soldier's words as he responded desperately, "The city has a self-destruct button. You hurt her; I'll activate it. Nobody'll get Atlantis!" It was a desperate last bargain, and an unconvincing one at that.

"Even if it exists, Major, you need at least two senior personnel to activate it - and I'm about to take one of them out of the equation." Kolya then brought his gaze to fall on Dr. Weir. He locked eyes with her and hesitated, but finally raised his weapon in preparation to fire. Dr. McKay fidgeted in the background, startled and scared, but unable to move. Scientists had always been soft and weak. Kolya's attention was brought back to the moment as the familiar radio crackled to life in his hands. He heard Sheppard's pleas and bargains but paid them no mind. He was now focused entirely on the scene unfolding before him.

The rain began in earnest, seemingly trying to pound his very flesh into the ground. He couldn't believe what he was hearing, what he imagined was happening. "Kolya?" McKay and Elizabeth were all the way in the control tower and he was powerless to do anything to help them, but he had to try. "Kolya?" Something…anything… "I'll give you a ship! I'll fly it out of here for you myself!" Please, please don't let this be happening. He waited with bated breath, but the wind was stealing it away anyway. The pounding rain continued, but he hardly felt it, every nerve in his body was focused on the radio in his hand, waiting for a sound but hoping it would never come. As silence continued to answer him, he knew there could only be one outcome. The rain was no longer the only thing causing a numbness to spread throughout his body. "KOLYA!"

"Kolya! Kolya, don't to this!" He tried again. The silence was killing him.

With a sharp crackle the radio unexpectedly came to life. "Major Sheppard. How's this for credibility? Weir is dead."

It was stated so simply, so coldly. John couldn't believe it, could hardly let it sink in to his saturated body. Elizabeth, his boss, his colleague…his friend. He'd let her down. He clenched the radio in a tight fist while he took a few deep breaths to compose himself. McKay was still alive, and he still needed saving, and John knew he was responsible for carrying out said rescue. Still, Elizabeth was dead and he could not, would not, take that lightly.

"I am going to kill you," he stated, his voice cold and lifeless.

"Maybe. Stay out of my way, or McKay will join her." The voice seemed untouched by emotion, seemingly unaware of the chain of events that had been set in motion. That was all the incentive he needed to get moving. He hardly took a last look at the brewing storm before heading back into the city. Sheppard was intent on saving McKay and, knowing they would only distract him, trying hard to keep thoughts of revenge out of his mind.

Ladon Radim, chief scientist of the Genii felt great pride in the fact that he was able to, albeit without much finesse, make use of the Ancient technology. He was fairly certain that he'd figured out the dialing device along with some sensors and various data terminals from which he was looking forward to downloading vital information. He was currently running what appeared to be a citywide body sensor and felt Sora looking over his shoulder. "He's moving."

Sheppard's lone dot on the screen moved towards three blinking Genii dots. They were going to intersect soon.

"Are you sure we're on the right level?" questioned a Genii grunt.

"Where did he go?" his companion asked.

"Shh! He can probably hear your stupid questions." Trust simple Genii soldiers to mess everything up.

Before the doors even opened Rodney could hear the rain lashing down. He saw the body of one Genii soldier, full of bullet holes. He looked away, knowing that soon he would find one more. Kolya was just behind them and Rodney had no choice but to let his traitor gene open the door and walk into the deluge. He glanced down to his left and saw the other fallen enemy, also taken down by P90 fire. His clothes were instantly soaked and as he looked over to Dr. Weir he could see that the same fate had befallen her, but at least she was alive. Holy crap, he just stood in front of a gun for her! But his thoughts were immediately disrupted as he caught site of the terminal.

"Oh, will you look at this?" He laced his voice heavily with pointed blame. He turned around to look at Kolya and saw Elizabeth, arms wrapped around herself in an effort to stay warm. "Oh, that is just ... that is just never gonna be useful again!" He was unbelievably pissed at this whole situation, and now he was soaking wet and cold, and there were bodies just a few feet away, and Elizabeth was out here with him and holy crap, he just stood in front of a gun for her. Okay, focus!

He pulled out his tool kit and set it on top of the panel. Squatting down and taking the cover off the panel revealed the many severed fiber-optic cables inside. After taking a closer look at the cables he turned and aimed a glare at Kolya.

"I should be able to bypass this switching station entirely."

"Good. How long?" No, not good, this was definitely not good. His fingers were already numb; he was cold, wet, miserable and being detained and forced to work at gunpoint. Things were most definitely not good!

"It's not half as bad as it looks. I'd say fifteen, twenty minutes tops." He surprised even himself with the steady, even keel of his answer. He could do this. Regardless of being held at gunpoint with an enemy force in control of the city, he still knew that this was the only way to save Atlantis. Getting Atlantis back under their control was another matter entirely, but saving the city came first and this storm was only going to get worse.

"Good," was the terse reply from the Genii military commander. No, no, no! Things were not good!

"We're in the eye," said the young lieutenant's unbelieving voice to his left.

"Right. Has to be," he agreed.

"The eye?" questioned the Athosian on his right.

"Dead center of the storm," he explained in his Scottish accent. "The storm swirls around a twenty to forty kilometer-wide area." His feet sank into the muddy ground and he was momentarily distracted from the clear blue sky to stare in horror at the destruction around them. Countless trees were down and the land was almost unrecognizable. It was a good thing that the Athosian village hadn't been around to be witness to this storm.

"Then this calm will not last," she correctly inferred. She was also now staring at the devastating affects of the storm. The look on her face was a mix of emotions but mostly she seemed grateful that her people had been taken to safety.

"No. In fact, in about ten minutes, it's gonna get very ugly again." Oh crap, this was shaping up to be a day full of surprises. What were the chances that the eye would pass directly over them? If Rodney were here he'd have calculated that factor in a matter of seconds. Unfortunately he was being held hostage at the moment and Beckett tried not to imagine the alternatives.

"Then come on, we have to help the major," exclaimed the young lieutenant suddenly. Ford turned around to run back into the Jumper, but was stalled at the sound of Beckett's voice.

"Aye, we can take off, but landing's twice as hard, believe me. What if the storm has reached Atlantis?" he questioned.

"Has it?"

"Not just yet, but it will any time now," he responded. He had a feeling he knew where this line of questioning was leading, he just hoped that he was completely wrong.

"Stop wasting time." The lieutenant roughly grabbed him and shoved him towards the Jumper, desperate to do something.

"But, Lieutenant..." he protested.

"Let's go!"

He tried to bargain, but knew it would be pointless as Aiden shoved him down in the pilot's seat. "We still have to fly straight through the storm, Lieutenant. It's insanity!"

"It's not insanity. This is a spaceship – we can fly up and over." Did the young officer have any idea of what he was saying?

"What, straight up and down?" His accent became thicker the more frightened he became. This was definitely insanity!

"Straight up and down," replied the Lieutenant Ford, making motions with his hands.

"I'm a bloody medical doctor, not a magician!" His day just went from bad to worse.

Sheppard, emotions pushed away from the surface, was on an adrenaline high. He had been running around the city nonstop for about an hour now, not counting the run to grounding station four before this whole situation became FUBAR. He had just successfully ambushed three Genii soldiers that had been tracking him. He assumed they had help from someone in the control room, but how the hell had they worked out the Ancient systems? No time to worry about that right now, he had a plan and little time with which to carry it out.

The Genii had switched radio frequencies after…well, after he'd contacted them on the one they were initially using, so he had been forced to return to search the bodies for another one. Just as he picked it up he heard Kolya's new orders.

"Radio Chief Cowen. Tell him to send reinforcements – a full company."

Oh, crap.

"Why did you tell him you could have this fixed in fifteen to twenty minutes?" Dr. Weir asked with more than a hint of exasperation. The fact that she was letting emotions break through her diplomatic façade meant that she was very shaken up. Hell, she'd just had a gun pointed at her, and McKay stood in front of it.

The man of her thoughts answered bitingly, "Oh, I don't know. Maybe, uh, so he wouldn't kill us?"

Elizabeth tried to be calm. "I understand that. But once the shield is operational, we won't be very useful, now, will we?" She was still thinking straight, that was something at least. Maybe if she wasn't so cold…

The look on McKay's face told her that he agreed with her logic. "Why did you let me tell him I could fix it in fifteen or twenty?"

"You just have to stall him some more."

"Well, I just told him how long it'll take!"

She did not need this right now. This had to be the most stressful day in history. More stressful than thinking they had to abandon the city, or finding out about Colonel Sumner's death, or even finding out about the life-sucking aliens that inhabited the galaxy. "Find another problem with it! I ..." She tried to think of some technical terminology, "...Tell them that the power loop interface isn't jiving with your walkabout! Something!" She threw words out of her mouth and hoped they made sense. She was freezing cold but knew that it was her responsibility to keep McKay in check.

"Isn't jiving?" McKay squawked indignantly with a look of disbelief on his face.

"Rodney, you get my point! Look, from the sound of it, if we can buy Sheppard enough time, it seems like he can take care of the rest of them on his own." She had high hopes that her second in command would come to the rescue. She had read his file and knew that he had black ops experience. She just hoped that he would show up to rescue the both of them.

"Radio Chief Cowen. Tell him to send reinforcements – a full company."

What? This was the worst possible thing she could have imagined happening right now.

"If you're hoping Major Sheppard can diminish our numbers, you are mistaken." At Kolya's statement, she and McKay shared a significant look of fear. She sent a silent prayer to whomever might be listening that they all made it through this alive.

'REALLY, REALLY DANGEROUS. DON'T TOUCH' – McKay

With a grimace at the sign, Sheppard turned to the Naqahdah generator and after a moment's hesitation, twisted and pulled out the control switch.

"Commander. Major Sheppard has cut power to the Control Room." Sora reported.

"How?" Kolya responded immediately. He listened to Ladon's explanation about the generators, but only one question came to mind. "Can you still track Sheppard?"

"No."

"Then we have no idea where he is now?" Kolya knew that this man was dangerous, and he knew that Sheppard would be extremely angry after his bluff. The Genii were slowly losing control of the situation, and to one man! He ordered Sora to take the necessary precautions and wait for reinforcements, and then he turned back to the Atlantians. "What's our progress?" The over-talkative scientist, McKay, jumped and stared at him fearfully, Before he could recover it was Dr. Weir who answered.

"We've hit a small snag," she reported as she stood to face him. "We're just running a diagnosis to make sure we can interface our codes properly."

Kolya had no idea what this diagnosis was or if it was even necessary. McKay had not mentioned anything of it. But, the military man also knew of many people like McKay, and people like McKay tended to lean towards self-preservation. Yes, this man was thinking of his own hide and would not dare risk his life and the entire city of the Ancestors with it.

"It's a small snag. Small. It'll take, like, half an hour at the most," the scientist finally spoke. A half-hour was hardly acceptable. The reinforcements would have arrived by that time and Kolya needed to show them that he was in command as they entered the city.

Without warning his thoughts were interrupted when the lights on the pier went out and Kolya was plunged into darkness.

"Commander, Sheppard has just disabled another generator."

"Yes, Ladon, I'm aware of that. He's cut the power to Grounding Station Three," he growled. Sheppard was causing too much trouble and causing him to become angry. He almost wished that he had killed Dr. Weir just to hurt him. Regardless, Kolya was sure that he still had the upper hand.

He quickly recalled what he was standing out in the storm for and turned on McKay. "Can it still be repaired?"

"Without power? No."

"Should we try and contact the major now?" the skittish Scottish doctor asked.

"The Genii may be monitoring our frequencies. We do not want to alert them of our presence," Teyla wisely answered.

"Aye."

Aiden took out a life signs detector and handed it to Doctor Beckett, it was useless to him without the gene. The doctor wouldn't shut up and stop complaining. Did he not understand how important this was? Beckett took the Ancient device and looked at Aiden curiously.

"Life signs detector," Ford explained, which he thought would have been obvious.

Beckett looked at the screen as it came to life and asked another stupid question. "These wee dots don't tell us much about who's who. How do we know which one's the major?"

Ford had a lot of faith and maybe a little hero worship in his commanding officer. "He'll be the dot getting rid of the other dots."

"How many should we expect?" he heard the young woman question. He had crept up the stairs to the control room without being seen. That in itself was a miracle.

"A full company – sixty or more," was the man's response. Great, how much worse could this day get. He'd thought of a plan during his mad dash to the control tower. Some may call it brilliant, in a time like this he might consider it just that, but it was still going to be impossibly hard, and not in a physical sense.

"I don't know how we were expected to take a facility this size with any less." Sheppard continued to crouch in silence, not daring to breathe as he waited for the incoming wormhole. He wished they hadn't gotten rid of the ten-thousand-year-old dead plants, they would have come in handy for some extra cover right now.

"It was supposed to be a raid to retrieve what was rightfully ours." His knees were beginning to cramp up and his mind was carrying out a silent battle of right and wrong.

The sound of the gate dialing and the familiar flush of the wormhole caused another necessary adrenaline spike.

"With me. Come on." This was better than he ever could have hoped for, there would be next to know one left up in the control room. But it didn't make what he was about to do any easier. As the girl and two other soldiers trotted down to the gate room floor, Sheppard picked himself up and walked up the last few steps slowly and silently.

"Reinforcements are arriving now, Commander." As the man continued to report, Sheppard crept up behind him, slowly coming closer without being seen or heard.

The first Genii soldiers started to materialize from the puddle and Sheppard knew he had to make his move soon.

"Have them secure Stargate Operations and report back to me."

The man answered a crisp, "Yes, Commander." As he lowered his radio and turned to go into the Control Room, Sheppard made his move. This would have to be swift and powerful to be successful. He used all the force he could muster and crashed a solid hit on the Genii soldier's temple, hopefully knocking him out. As the man fell, Sheppard caught him and silently lowered him the rest of the way to the ground. His heart was pounding through his chest with the possibility that someone noticed his presence, but a quick check down to the gate room floor proved that he had been lucky. He counted five Genii soldiers that had come through the gate during his scuffle and knew he could not afford any more. He ran behind the dialing console and with the simple touch of a button the gate shield was raised.

"Secure the area. Then I want you to ..." the woman trailed off as the shield activated over the puddle. Sheppard grimaced from his lookout in the control room as impact flashed began to strike the shield.

"Turn it off, Ladon!" came the disbelieving shout from the floor. He saw the woman turn around and register that this Ladon was nowhere to be seen.

Wrong.

Something impacted him and he fell heavily to the floor with what he realized was the weight of a body pressing down on him. The air was knocked out of his lungs and he gasped for a breath. His P90 went flying and a powerful fist struck his face.

So, not knocked out after all.

"What did you do!" an angry voice commanded from above his head. He heard footsteps running up the stairs mixed with more impacts against the shield. He was struck again and then roughly pulled to his feet by many different hands.

"Fix this, now! Lower the shield!" shouted the woman desperately.

Sheppard head was still reeling from the punches he'd taken and he had absolutely no desire to comply with her order, despite the number of lives being lost due to his actions. These people had taken over his home, killed his friend and still held another hostage. There was no way he would be helping them any time soon. Some nameless soldier punched him in the gut when he didn't move and he doubled over, but hands held him up and he felt someone snatch his sidearm from it's holster. As he tried to suck in enough air to satisfy his lungs he heard the woman having a heated discussion over the radio, probably with her commander.

After some command or other must have been given, he was roughly thrown toward the DHD and gripped it to keep from falling.

"Lower the shield or Doctors Weir and McKay die!" The woman didn't realize her mistake until too late.

"Weir's alive?" Sheppard asked incredulously. The seconds ticked by so slowly as more impacts could be heard against the shield. Weir was alive! Kolya had been bluffing. Impossible. The cold-hearted bastard was actually bluffing. Sheppard's world narrowed to this one wonderful fact and blocked out everything else, that is, until the gate shut down.

Chaos erupted around him as the soldiers screamed and raged for their lost friends and brothers. Expecting the inevitable, Sheppard was ready when the small mob attacked him. His mind slipped completely into military mode mixed with fight or flight, and only one of those was possible right now.

His P90 and 9 mil were long gone, but he still had his military issue knife. He quickly grabbed it in his right hand and brought up his left to block a fist flying toward his face. An unlucky soldier directly in front of him got slashed in the belly and Sheppard was grateful that he had the DHD console to cover his back.

He also counted himself lucky that he had been sparring with Teyla regularly, well, semi-regularly. He continued the slash to block an uppercut with his right forearm, a move that Teyla would have been proud of. But there were too many bodies being forced upon him in all directions and his left side was now vulnerable. The Genii quickly overpowered him and landed several blows to his face and a few to his ribs, which blossomed in pain. A kick to the back of his legs sent him to his knees and a few more well placed boots in his midsection had his forehead pressed to the cool Atlantian floor struggling for air.

Blood was freely dripping out of his nose and a split lip. It hurt to breathe, which probably meant cracked or maybe broken ribs. Most of the pain was in his left side. It was only when he realized that he had time to catalog his injuries that he registered the halt in the soldiers assault. Another booted kick to the ribs had him sprawled on his side, his face twisted in agony, struggling for air. God, he wished they would stop doing that.

"Leave him be," he finally registered a coherent sentence coming from somewhere above him, just as another kick landed in the small of his back.

"I said leave him be, Mohan!" Sheppard tried to shy away from the direction of the last kick but just ended up curling further into himself and coughing raggedly, still gasping for a full breath.

"But Sora, my brother and cousin! Both –"

"Commander Koyla wishes to deal with Sheppard himself. Leave him be."

Shit, that couldn't be a good sign.