First time submitting a story, so I will apologize now for any faux pas that I commit going forward. Like many, I began writing alternative histories in my head following the ending of Mass Effect 3. With Mass Effect Andromeda drawing nearer I have been thinking of this again. I finally worked up the courage and desire to write this out. Also, I don't want it to exist only in my head. So, thank you to anyone who takes the time to read this so many years after the release of Mass Effect 3 and I hope you do not feel your time was wasted. The story picks up at the death of Kai Leng and flows from there with many obvious changes. Since I have seen numerous others note this I will state I do not own these characters and I thank the writers and programmers at Bioware for creating them.


Chapter 1 - Suspicions

As the "Rimmer" model hard light omni-blade winked out of existence, Shepard watched the thin layer of blood that had been clinging to it fall and spatter across the corpse of his fallen enemy. Kai Leng had been a bastard in life and fully deserved the end he had received, but he had been one other thing that robbed Shepard of any satisfaction in his victory. Indoctrinated. The word echoed in Shepard's mind. Vendetta, the Prothean virtual intelligence he had failed to obtain during the fall of Thessia, had stated as much, reconfirming the statement here aboard The Illusive Man's space station. Shepard had confirmed with his Prothean crew member, Javik, that the VI was indeed capable of such detection.

Following his failure on Thessia, Shepard had thought only of what had to occur to retrieve the VI and learn the information necessary to complete the Prothean super weapon that Alliance scientists had dubbed the Crucible. He was focused, desperate, and unhesitating. He and his crew had invaded the supposed safe haven of Sanctuary and learned of the horrible experiments Cerberus had performed on its refugees in the name of controlling the Reaper's minions and, ultimately, the Reaper's themselves. With the help of Miranda Lawson, Shepard's friend and a former Cerberus operative, he was able to track Kai Leng to the hidden space station of the Illusive Man, the mastermind of all Cerberus operations and projects. But he had again been too late. The Illusive Man had learned that the missing component of the Crucible, the Catalyst, was in reality the enormous space station that served as the center of galactic government and culture, the Citadel. The Illusive Man had learned this information, transmitted it to the Reapers, and vanished leaving behind his minion to attack Shepard and his crewmates.

Shepard struggled to make sense of the pieces of information. He knew The Illusive Man craved power for himself, for Cerberus, and ostensibly for humanity. It was no surprise that he would seize the Prothean VI and take for Cerberus the secrets it contained. It seemed he had obtained what he wanted. But then he had handed the information over to the Reapers. That, more than Vendetta's assurances, convinced Shepard that The Illusive Man was indeed indoctrinated. He was not a man to give away anything, let alone the key to power and, hopefully, the defeat of the Reapers. But if he was indoctrinated, then it was the Reapers who controlled him, feeding him fantasies of human dominance to keep him attacking the Alliance and the other races, turning even the supposedly safe haven of Sanctuary into an abbatoir. But if he was indoctrinated, why leave Vendetta behind if there was even a chance of Shepard retrieving and using the VI? Why sacrifice a powerful and reliable minion such as Kai Leng?

Shepard's mind was roiling with questions and doubts. He could not know when The Illusive Man's indoctrination occurred. It could not have been prior to the destruction of the Collector base. That had been orchestrated by The Illusive Man and resulted in the elimination of an enormous resource for the Reapers, including a partially constructed human-based Reaper. Unless The Illusive Man's failed efforts to keep the base intact represented a ploy to put the base in indoctrinated human hands. Shepard shook his head as he struggled with competing scenarios. If a mind as brilliant as that of The Illusive Man could be so manipulated, what did that say about Shepard's own decisions? Shepard had always considered himself a simple soldier, albeit one with a keen tactical ability and exceptional combat skills. Ever since the Reaper attack on Earth, Shepard felt like he had been trying to catch up with events. It occurred to him that often when one is behind it is because one is being led.

A shudder went through the station snapping Shepard out of his reverie. As he was struggling with his grasp of events, the Alliance bombardment of the station was continuing. Remaining on board was becoming more and more dangerous. Shepard looked from Kai Leng to the companions that had recently helped him defeat the Cerberus minions. EDI, an artificial intelligence housed in a feminine, robotic body, was scanning the computer systems for any additional information. Tali'Zorah vas Normandy, the Quarian engineer who had stood by him throughout his ordeals and become much more than a crewmate, was standing guard with her shotgun at the ready, a combat drone orbiting her protectively. Shepard put aside his thoughts, but knew his mind would keep worrying at his concerns until he could make sense of them.

"Time to go", he bluntly stated. "EDI, bring every bit of information you found and make sure to bring Vendetta". Shepard paused a moment, "Make sure there are no booby traps in the data or the VI. The last thing we need is to fall into that sort of trap again".

"Yes, commander", EDI stated. "Data and VI acquired and ready for transport. No traps detected."

"Good. Inform Admiral Hackett we are moving to the extraction point and", Shepard looked around the room, "Find me whatever secret elevator, or stairs, or laundry chute The Illusive Man uses to get in and out of here. There's no way he was climbing ladders and ramps every time he wanted to come to his office".

A short elevator ride later and Shepard found himself not far from the hangar bay through which he and his comrades had initially invaded the station. The Cerberus troops had been scattered or killed, leaving only the beachhead that Admiral Hackett had maintained as an extraction point. There was no intention to take the station. With EDI in possession of what information could be taken from the computer as well as Vendetta, the station was one more piece of Cerberus that the Admiral intended to obliterate. Shepard boarded a new shuttle with his pilot, Steve Cortez, at the controls. "Next stop, the Normandy", Cortez called back to his passengers. Shepard did not react, he was already further considering the information he had learned, trying to plan what to do next. He had been staring at a blank bulkhead for several seconds when he felt a gentle touch on his leg.

Shepard turned and looked into the glowing spots that were Tali's eyes, all he could really see of her face through her helmet. He could picture her face within. She had removed her helmet and shared her true appearance with him when they became lovers prior to the destruction of the Collector base. Her turned his full attention to her, picturing that beautiful face tense with worry.

"You're going to give yourself worry lines squinting like that", she chided. Her light tone masked her worry, but Shepard had come to know her well enough to read the tension in her body language and tone.

"I was just thinking the same thing about you", Shepard joked back.

"Another advantage of a Quarian environmental suit, no worry lines", she paused, "at least none visible".

With that last statement they both let the feigned lightness of their moods drop. She removed her hand from his leg and took his hand between both of hers. "I can see the tension in you Shepard, we'll get the Citadel from the Reapers and use the Crucible somehow. We have to".

Shepard could feel Tali straining for some way to reassure him, to comfort him. And she was right. With the Reapers having taken the Citadel and moved it to Earth, their only hope was to bring the Crucible to Earth and somehow link it with the Catalyst and, then what? Profit? Every scientific source in every participating species claimed the Crucible was immensely powerful and contained enormous quantities of energy that could be released, but no one was sure precisely what form that release would take. Everyone seemed to take it on faith that this would be powerful enough to somehow defeat the Reapers. Apparently, the Protheans thought so. So did multiple previous civilizations who had attempted to build and deploy the device. None had succeeded. The collected species of this cycle intended to be the first, but Shepard realized there were an awful lot of ifs. He also realized he had drifted into his thoughts again and that Tali was sitting and patiently holding his hand while he worked through his thoughts.

"Apologies", Shepard said, "I have a lot on my mind about how we are going to manage to pull this off". "I feel like we're doing everything we can and we'll get the Crucible to the Citadel and access the Catalyst somehow, but I've got my concerns too". Shepard would never voice these thoughts to the crew as a whole, but Edi had withdrawn to give him and Tali privacy and Cortez was busy piloting the shuttle. Before Tali had become his lover, she was his friend and confidante. Talking with her seemed to help his thoughts flow more easily, maybe even to help untangle his current doubts.

"I can see your concern", she stated, reaching up to rub the crease between his eyebrows. "I've never seen anyone pick apart a tactical problem the way you do, Shepard. Give me a beat up skycar and a few hours and I'll make it capable of flying us to the migrant fleet. That's where my talent lies. Trust your talent. Trust your gut, as you say. If you have worries, then keep picking at them. If you have doubts about how plans are being executed, then start coming up with other options, other contingencies. I'll back you up whatever you decide to do. The whole crew will". She said that last with clear conviction and Shepard knew she was right. About all of it. The crew trusted him completely and would follow him into and through whatever hell awaited them. Which meant he could pick apart his doubts and make contingencies knowing he had the resources to execute them if necessary.

Shepard suddenly turned and took Tali into a full embrace, hugging her closely to himself, engulfing her petite body with his much larger frame. He just held her like that for several seconds, holding tight to her in the midst of everything. He finally released her and held her at arm's length by her slender shoulders, looking into those glowing spots. Finally he whispered, low and just for her, "I love you, Tali. I am a better man when I'm with you and I'm glad I finally realized how much you mean to me. And you are right. I need to work through my concerns and making contingency plans will help with that. I wish I had been doing that all along, but I can't change that. I can only go forward. The next thing I need to do is pay a visit to Admiral Hackett. Along with Vendetta."