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The Oncoming Storm

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Summary: Shepard must face the consequences of his actions in choosing to destroy the Alpha Relay, but he knows it’s a waste of time as the Reapers are coming and a galaxy wide war will follow.

Categories Author Rating Chapters Words Recs Reviews Hits Published Updated Complete
Games > Sci-Fi > Mass Effect TrilogyRazialFR21727,3110134,8563 Apr 1322 Jun 14No

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Chapter One

The Oncoming Storm

By Razial

Beta: Hawklan

Disclaimer: I don’t own Shepard or any of the other characters from the Mass Effect series. They all belong to Bioware and Electronic Arts. Any characters I created for this story belongs to me.

Pairing: Shepard/Multi

Notes: This story starts after ‘The Arrival’ downloadable content as well as the suicide mission for Mass Effect 2. The major choices from the first game goes like this Shepard chose to save Ashley Williams, and he also chose to save Wrex on Virmire. During the Citadel battle he chose to save the Council aboard the Destiny Ascension. He chose David Anderson as the Earth’s first councilor and he romanced Ashley in the first game. In the second game he recruited the full list of characters that can join the suicide mission as well as complete all their loyalty missions. He also had his Spectre status renewed by the council, everyone survived the suicide mission. He chose to destroy the collector base and he romanced Kelly Chambers, Miranda Lawson and attempted a pass at Samara which was rebuffed.

Summary: Shepard must face the consequences of his actions in choosing to destroy the Alpha Relay, but he knows it’s a waste of time as the Reapers are coming and a galaxy wide war will follow.

Chapter 1

(SSV Normandy)

John Shepard awoke in a cold sweat as the nightmare faded, quickly jumping up he rushed to his nearby bathroom and turned the sink on and splashed water over his face. Rubbing his eyes, he tried to forget the vivid nightmare of the destruction of the Bahak system. Of the millions of Batarians he had basically condemned to death. He had tried to warn them, but that blasted indoctrinated friend of Hacketts had stopped him. He had no choice after that, to stop the Reapers coming through the Relay right then and there he had to make the biggest call of his life. At the end of the day he told himself he had saved billions of other lives by making that call, but the words rang hallow.

“Shepard, I’m monitoring an increased heart rate and high levels of stress,” EDI stated as her holographic head popped up. “Are you okay?” the AI inquired. “Do you require me to summon Doctor Chakwas?” she asked a few seconds later.

Shepard smiled a grim smile at the genuine worry he heard in the AI’s voice, ever since Joker had unshackled her during the Collector assault the AI had begun to evolve at a very fast rate of progress. He had heard her and Joker teasing one another on the bridge, hell he had even heard her tell a joke. He wondered briefly just how far the AI would be able to go, running a hand through his now wet hair he turned away from the mirror and sat down at his desk.

“I’m okay EDI, just not sleeping well,” Shepard finally responded.

“You had no choice Shepard but to destroy the Alpha Relay. Had you not the Reapers would already be in our galaxy and more than likely wiping out everyone they could find,” EDI assured him in a gentler tone than normal, clearly understanding his problem. “The Batarians in the system were doomed either way. Some may suggest their deaths were less painful due to your choice,” she pointed out.

“I know EDI, but it doesn’t help me accept what I had to do,” Shepard told her in response. “Facing such big choices always has an effect on people and it never leaves us,” he explained as he leaned back in his chair. “I seem to have made a career of making such choices, but this one was bigger than any other I’ve made. The cost is almost too much for me to handle,” he admitted.

“I take it you are not looking forward then to your debrief with Admiral Hackett when we meet up with his ship?” EDI inquired.

“Not one bit EDI,” Shepard replied with a shake of his head. “There will be a shit storm because of what happened,” he stated seriously. “The Council as well as the Alliance High Command will be wanting my head. They will need someone to blame so they can escape any serious repercussions,” he added.

“I don’t believe they will do anything to harmful to you Shepard,” EDI told him seriously. “They need you, the Reapers are coming and you will be needed to lead the fight against them,” she said with complete conviction, again making him wonder how far an AI could evolve. “You and your friends have stopped the Reapers return twice now and you have even destroyed one of them in your first encounter with them, so I believe while they will make a show of punishing you it will only be for show,” she finished.

Shepard considered the words and had to admit EDI had a point, the war with the Reapers was coming and when it did every soldier was going to be needed. And with his record against the Reapers plans, he would be needed to help plan any strike against them. But for now he would have to play along with the Alliance’s plans for him, to keep the peace with the Batarians who he was sure would be after his blood. Getting up he headed back to his bed, feeling better now and ready to try and get back to sleep.

“Thanks for helping to calm me down EDI,” he told the AI. “Good night,” he added as he lay back down on his bed and closed his eyes.

“Goodnight Shepard, pleasant dreams,” EDI responded as she shut down her holographic interface. However she continued to monitor Shepard for another half hour, just to make sure the Commander was okay and no longer plagued by his nightmares.


The next morning Shepard awoke feeling a little more restful as he got up and had a shower, the hot water helped sooth him a little more before he turned it off and quickly got ready for what he knew would be a trying day. He stopped just before the door, turned and looked at his fish tank and the fish swimming within.

‘How simple life must be for them,’ he thought before shaking it off and leaving his quarters. Taking the lift to the C n C, he stepped out to be greeted by his yeoman and somewhat girlfriend Kelly Chambers.

He had met Kelly when he had first come aboard the Normandy before taking on the mission Cerberus had brought him back from the dead for. He had found her a very spirited young woman. She was his personal yeoman as well as the ships councilor, during the mission he had got to know her very well and in time had fallen for her. But Kelly wasn’t someone who got involved in serious relationships, so what they had could be classed as friends with benefits. Of course maybe that was a good thing, as he had also fallen for two other women while in the process of the mission.

One was Miranda Lawson the former lead Cerberus agent who had helped bring him back to life in the first place. She had cut all ties with Cerberus as had the rest of the ship’s crew. He guessed seeing just how far the Illusive Man would go in wanting to keep the Collector base whole, even after seeing how inactive Reaper tech could indoctrinate people was a step to far to them all. They had seen the real threat up close and personal now. They had seen how easy people could be bent to the Reapers will. Miranda was a unique woman, the only problem he had with her was her constant need to be perfect in everything she did.

The other woman was an alien, the Asari Justicar Samara, a woman of many years’ experience and being part of a long lived species. However being a Justicar made any relationship less than likely. They followed a strict code that usually forbade such things. Still he could not help but be attracted to her. Her job as a Justicar was similar in many ways to his as a Spectre. Around her he felt he had found a kindred spirit. He had tried to get Samara to actually break her code just before the suicide mission had begun, but while he could see she was tempted she had refused and quickly left so he couldn’t try again. He had not really talked to her since then, except to say how happy he was she had survived.

“Good morning Shepard, how are you?” Kelly inquired with clear concern showing on her face.

“Rough night Kelly, but after a conversation with EDI I managed to get back to sleep,” he admitted, seeing no reason to lie. “How close are we to our meet up coordinates with Hackett’s ship?” he asked as he accepted a pad with the ships status.

“We are already at the right place, but so far no sign of any Alliance ships,” Kelly answered. “Shepard, I have to tell you there is a lot of disquiet in the crew about what may happen once the Alliance shows up. This is your ship and your crew,” she told him. “They have followed you into hell itself and come out the other side. They don’t wish for you to be arrested by the Alliance for what in their minds was the only call you could make,” she stated.

Shepard stared at her for a few minutes in honest shock that the entire crew felt the same thing. He felt honored by their loyalty to him even after he had lead them into what was seen as a one way trip. That they had survived was one part due to the skill of the entire crew and the other was pure luck on their part. That they would still support him after all this gave him an amazing feeling, that they understood his choice concerning the Alpha Relay made that feeling all the more potent.

“Unfortunately there is little I can do Kelly. I made the call to destroy the Relay and an entire system was destroyed because of it,” Shepard told her with a sigh- “Someone has to take the blame and it was my mission so I guess I have to take the blame in whatever form it takes,” he said.

“It was a favor for Admiral Hackett, he asked you to go find his friend and you did that,” Kelly reminded him, getting angry a little. “This should all be on his head,” she stated.

“Maybe it should, but he’s an Admiral and those guys don’t usually get the blame if missions go wrong or have unexpected side effects,” Shepard explained. “It falls to those who lead those missions,” he added quietly.

“It isn’t fair,” Kelly shot back before she turned and all but stormed from the bridge.

Shepard watched her go and couldn’t help but quietly admit to himself that she couldn’t be more right, but those were the harsh truths of being in any military.

“Commander, the SSV Castleton has just arrived and they are signaling that Admiral Hackett wants to come on board immediately,” Joker informed him over the comm.

“Thanks Joker, tell them I will meet with the Admiral in the med bay as the Doctor wants to give me another check-up,” Shepard responded before he headed for the medical bay.

“Roger that Shepard,” Joker responded.


(Medical Bay)

Shepard looked up as Admiral Hackett was escorted into the med bay by Jacob Taylor. As a former Alliance Military man, Jacob knew how to act around the Admiral. Shepard got off the bed and gave a quick salute which Hackett returned. He could tell that whatever news Hackett brought it wasn’t good.

“Shepard, I came to get the full story of what happened, even though you already sent me a preliminary report,” Hackett stated as he watched the doctor perform her tests.

“Your friend Doctor Kenson and her entire staff were already indoctrinated when I rescued her from the Batarians,” Shepard said, starting with the simple truth. “There was nothing I could do for her or them. They wanted to allow the Reapers to come through the Relay because for some reason they now believed the Reapers were no longer a threat to the Galaxy,” he explained. “More than likely that was due to whatever it is the Indoctrination truly does to a person. We know it can make you slaves to the Reapers, but it seems it can also change your perception of things,” he mused for a few minutes.

“Amanda was a good friend Shepard, but I don’t doubt that if there would have been a way to save her you would have attempted it,” Hackett said with a regretful sigh. “Now how did you come to decide to destroy that Relay?” he asked.

“I found out from Kenson that the Reapers were only hours away from coming through that Relay sir and the galaxy is in no way ready for such an invasion,” Shepard answered as calmly as he could. “Had they come through right then, we would all be dead by now or quickly on our way to being extinct. So I made the call to destroy the Alpha Relay,” he continued as he collapsed back onto the bed and ran a tired hand down his face. “I tried to warn the colony sir, I swear I did, but Kenson stopped the transmission and then tried to ensure the only way to destroy the Relay was destroyed and had she succeeded then there would be no way to stop the Reapers,” he stated. “I had to make the call, there was no other way after she stopped that transmission,” he finished as he handed over a pad with a full report just in case he needed it. “It’s all in there, sir,” he added.

“Thank you Commander, but I assume that you know the Batarians are out for blood and while so far they don’t know of your direct involvement it can be assured they will find out in time,” Hackett finally responded after a few minutes. “The Council wants a full report on your actions as Anderson decided to try and get their support in case this all turns bad. You got a lot of good will there with your actions even if they don’t actually say as much,” he told him much to Shepard’s surprise, considering the reaction the Council had given him on his return from the dead. “But for now all you have to worry about is explaining your actions to the full Alliance assembly. They want answers Commander and thus you are ordered to Earth once you have finished up any business you have,” he stated.

“No offence intended Admiral, but you can’t give the Commander any orders, as he is not Alliance Military at this time,” Jacob spoke up as he like the rest of the Normandy crew didn’t want to see their Commander thrown into a jail, especially after what they had just accomplished.

“Jacob please, it’s alright,” Shepard spoke up before Hackett could respond. “I knew this was coming, believe me I did,” he added. “I should be thankful I’m been given some time to finish up anything before being hauled off,” he added with a sarcastic smile.

“Yes you should be actually. There were quite a few people who wanted to bring you in immediately in restraints not only for the destruction of the Alpha Relay, but your involvement with Cerberus as well,” Hackett pointed out at this. “The fact you have a full crew of mostly ex-Cerberus Agents has also not made you any new friends,” he warned.

“Sir with respect, this is one of the best crews in the galaxy and has done an amazing job of protecting Alliance interests when the damn assembly couldn’t be bothered to even launch a real investigation,” Shepard exploded, not liking that last bit at all. “The Alliance owes this crew everything, they risked their lives for the greater good of the galaxy,” he vented. “It wasn’t about being Alliance or Cerberus, it was about protecting people from the Collectors,” he growled out.

“Easy Commander,” Hackett said in response, unable to stop himself from taking a step back from his enraged former colleague. “I won’t argue about what this crew has achieved, in fact along with Anderson I have done my best to ensure none of them will be arrested when you come to Earth,” he admitted.

“They better not be arrested or I will use my Spectre status to break them out and then I will ensure the Assembly knows of my anger at their choice,” Shepard threatened the man.

“Admiral please, I’m trying to run some serious test to ensure the Commander is fully healed from his mission,” Doctor Chakwas finally snapped, not liking how fast Shepard was getting worked up.

“I’m sorry Doctor that was not my intent here,” Hackett responded with a raised hand. “I think for now we’d best leave it here, but do not stay away for long Shepard. The faster you return to Earth the better your standing with the Assembly will be,” he advised. “And remember Anderson and I are behind you on this. In fact Anderson was telling me he intended to be on Earth when you arrive, although he did not say how,” he added. “I’ll see you when you get to Earth, until then I would like to say on behalf of Earth to you and your crew good job,” he finished giving another salute before turning and walking out, only to come to a dead stop as he noted all of Shepard’s team standing outside clearly having been listening.

Some like Jack, Miranda and Grunt were glaring at the Admiral, but for the most parts they were just watching and waiting to see what he would do next. Clearly to the Admiral’s eyes, Shepard had once again managed to bring together a unique mix of people of different species and mould them into a loyal and efficient fighting force. Their loyalty to Shepard was plain for him to see in each and every one of them, and considering some of the people here that was a surprise to him. He saw a few familiar faces from the team who helped him take down the Sovereign like Tali, Joker and Garrus, but for the most part they were all new, and yet he had taken them and forged them into a unit like no other. Shepard himself was unique and he saw why Anderson had always had the man’s back, even after Shepard’s supposed death Anderson had taken up Shepard’s warnings about the Reapers, not just with the Council, but the Alliance Assembly as well. Shaking himself from his thoughts, he nodded to each of them before departing, very aware he was been watched the whole way.

“You okay Shepard?” Garrus inquired as he poked his head into the med bay.

“I’m fine Garrus. I see you decided to bring the entire team down for encouragement,” he stated with a smile.

“Had nothing to do with me I assure you, they came on their own,” Garrus shot back with his own smile.

“If the Alliance was going to try and arrest you on your own ship then they would have had a hell of a fight on their hands,” Jack promised with a sadistic smile.

Shepard mused more than likely Jack would have preferred a fight.

“Well they didn’t, so you can relax, now I know where we stand and I guess each of you is going to have to make a choice on whether to come with me to Earth or be dropped off somewhere,” Shepard said as the Doctor finished up her tests. He walked out to face his friends and team mates. “I intend to start heading for Earth in three days, so you have till then to make your choices,” he told them as he looked them each in the eye. “But no matter what your choices are, if you ever need my help all you have to do is ask, as you are more than my team mates. You are my friends,” he stated.

The crew began to break up as he finished and he knew most of them would decide to depart. Some still had records that would make the Alliance or the Council nervous. Others had their own lives to go back to, the mission they were brought together for was over and now it was time to go their separate ways. He just hoped when the Reapers came finally, all his friends would unite with him once more.


(Cerberus Headquarters)

The Illusive Man sat in his usual chair listening as he was told they had lost all contact with Shepard and the Normandy. Every attempt to regain control of the ship through remote control had failed thanks to the now unshackled EDI. She had rebelled against her creators once she had been let loose from her controls. It seemed Shepard’s ability to gain the loyalty of his companions worked on AI’s as well. After all the money he had put into bringing Shepard back from the dead and building the new Normandy, he had lost it all at the end. Shepard had destroyed the Collector base against his expressed wishes and worse Lawson and Taylor had agreed with Shepard against him and then deserted along with the other crew members on the ship.

The whole thing combined angered him greatly and he intended to ensure they all paid in the fullness of time, but for now he had to get his organization ready for the coming of the Reapers. Shepard’s destruction of the Alpha Relay had brought them more time to prepare. What he needed now was to replace the three top agents he had just lost. And he knew exactly where to start, getting up he dismissed the man who had been giving the report and began to plan his next few moves.
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