So I noticed in the Indoctrination Theory that the whole thing ends (in the ideal) with Shepard waking up before the whole Conduit thing starts. So that still leaves a significant amount of story untold. Such as if and how the Reapers are actually defeated and what happens after Shepard wakes up and assuming they survive, how would the Normandy crew spend the rest of their lives? This is my attempt to answer those questions in a manner that still mostly supports canon. I hope you enjoy reading this and the control/synthesis ending version that I'll be putting up shortly.
Destroy Ending
Shepard woke up. She inhaled sharply. Everything hurt. All she remembered was the heat of Harbinger's laser and then the dream. It can't have been a dream, yet it must have been. Shepard felt weakened, yet she felt lighter at the same time. Like a burden over her head had suddenly vanished. When she finally opened her eyes, she was almost relieved to see that the greyed skies of London remained as dull as when she had lost consciousness, making it easier on her eyes. Beyond her, she saw something that made her already weak heart stutter. Garrus, Wrex, Grunt, Tali, Kasumi, Zaeed, Jack, Miranda, Kaidan, Jacob, Samara, James, Javik. Liara. Shepard wanted to scream at her bondmate to get back aboard the Normandy, that it wasn't safe. Yet she felt the dryness in her throat and the heavy ash in her lungs and she couldn't speak. She knew that Garrus was speaking. He'd grown so much, he'd become a leader. Shepard just wished that she could hear his undoubtedly rousing, powerful speech. All she heard was the ringing. All she felt was the agony and the burns scorching across her body. All she could smell was the burning and the ash and the smoking rubble that surrounded her.
Liara spotted Shepard first, because of course she would. Her eyes darted back towards the Normandy.
"Get her to Chakwas!" She ordered two soldiers from the Normandy, Garrus saw what the commotion was about and smiled widely.
"Now that she's safe, it's time for us to finish off the Reapers. For Shepard!" He held his rifle in the air. They had gone over the plan countless times.
"For Shepard!" Came the reply, whether it be roared, yelled or screamed. Rifles and shotguns and pistols were waved in the air and Garrus knew that they were ready. Everyone had been eager to join. EDI wanted in on it too but they'd insisted that the ground team would have enough tech experts as it was and if Joker couldn't handle a sudden Reaper attack, EDI would be able to.
"Positions!" Garrus ordered as Grunt and Wrex charged ahead first, with Jack following closely behind and putting up a barrier to protect the charging Krogan. Tali ran directly behind them. Zaeed and Jacob ran slightly behind and surrounding Tali to protect her as she was their designated tech expert to get the crucible up and running. Further back, Miranda, Javik and James ran with Kasumi and Liara who would be their backup if Tali was injured or killed. Finally, right at the back of the pack was Garrus with his sniper rifle and Kaidan to protect him with biotics. Kaidan would also be their final line of defense if something happened to both Tali and Kasumi.
The squad charged ahead into the conduit.
When they awoke again, they found themselves in Citadel tower, nearby to the control panel that Garrus and Kaidan recognised as the location where they fought against Saren. The main control panel lay ahead of them and the group forged forwards with the biotic users forming a circle of barriers around Tali, Liara and Kasumi and those who used physical weapons blocking off all entrances to the area. Garrus pointed his scope dead down the hall, watching for the elevator in case it arrived full of husks or banshees.
"Admiral Hackett, the Citadel is open. Send in the Crucible." Garrus reported as the Citadel opened around them, revealing a battle scene unlike any he'd seen before. Indeed, Earth had taken perhaps even more punishment than Palaven. The Crucible docked and Liara, Tali and Kasumi set about working the ancient device. Whilst they worked, husks suddenly began to swarm the squad. Grunt, Wrex, Zaeed, Jacob, Javik, James and Garrus opened fire and thanks to the biotic barriers put into place by the rest of the squad, the husks never got close. There was a close call when a Brute showed up, but everyone survived. These were damned competent soldiers and they acted like it. Then the Crucible opened fire, and it was like nothing any of them had ever seen before. A grand pulse of blue electricity fired out from the device. It didn't seem to affect any of the ships, probably due to the complexity of the device. Well, that was a lie, it affected some ships, namely the Reapers. Giant destroyers of races just stopped moving as the pulse overwhelmed their systems. Some fell from the sky, colliding with the great oceans of Earth at high speeds, undoubtedly causing tsunamis on Earth. They wouldn't complain about a few tsunamis after surviving the Reapers. Some Reapers remained in orbit, stripped of movement and power. After the last Reaper fell, a beam was sent to the mass relays which amplified the pulse towards other systems. The Reapers would fall in every system.
It took a solid two minutes of silence before the strike team on the Citadel heard whooping and cheering over their radio. The Reapers were defeated! Wrex was the first to react on the ground team, he pounded Grunt's shoulder in a congratulatory manner. Grunt replied to this by laughing and hugging the clan leader. This feeling of overwhelming joy then spread throughout the group. Zaeed and Kaidan grasped each other's hands in a brotherly manner and pulled each other in for a half-hug. Javik sat down, placing a hand to his head, astounded that they had stopped he cycles. Jack and Miranda stared at each other for five solid seconds before smiles overwhelmed their past grudge.
"Fuck it!" Jack exclaimed as she hugged Miranda. James and Jacob high fived and leant back against a railing, finally catching their breath. Tali and Kasumi hugged each other tightly, knowing how important a role they played and that without Shepard, they'd never have gotten this far. Garrus and Liara stared each other in silence. Of course, they smiled knowing that thanks to them, the galaxy's greatest threat was being wiped out as they stood, but they worried for Shepard. After all, she was the one who got them there. When Harbinger saw Shepard dead, they assumed that the Galaxy would die with her. After all, synthetics don't know hope like organics do.
"Vakarian to Normandy, Joker come in."
"You did it! You crazy bastards did it! Chakwas said Shepard will be okay too. Head to Huerta Memorial and you can meet Shepard there, she'll need some patching up but she's survived worse. Then we can head to the Normandy for some drinks, how about it?" Joker's words over the intercom were a relief to say the least. The Reapers were gone, Shepard was alive, everyone would live. It was thanks to Shepard too. Without her, half of them wouldn't be there to even see the end, much less be a part of it.
When they reached the Normandy, they found a crate of varying alcohols outside with a note saying 'You've earned it, Anderson'. James and Javik lifted the crate and carried it aboard the Normandy. When the airlock had finished with the decontamination process, the ground team saw a proud smirk on the face of their commanding officer, Shepard had a crutch and severe burn wounds, but she'd survived worse. She pushed herself upright and saluted her friends. At least, she remained upright until Liara got hold of her and she had to lean against a wall to remain on her feet as the hug she received had winded her. Garrus and Shepard shook hands and exchanged a smile.
"I'm glad you came back in one piece Garrus. There's no Shepard without Vakarian." Shepard congratulated her old friend in her own way. "Shame we couldn't have finished the Reapers off together, but you can't win them all."
There was one hell of a party. Of course there was. Wrex and Grunt were sober throughout, having bad memories of their last morning after partying with the Normandy crew. They still enjoyed themselves nonetheless, watching the rest of them get drunk was a sight to behold. Vega did so many shots that he passed out in the women's bathroom, shouting that it was cleaner than the men's. It probably was before he got there. Kaidan finally got his Canadian lager, which he happily shared with Shepard. The Asari didn't drink, so Samara and Liara were babysitting all evening or discussing things with each other such as Thessia, and what would become of the Asari race. Javik and Liara also got in some interesting conversations about writing a book about everything people didn't know a both Protean culture. Liara admitted that it may shamefully be more about her own interests than public interest.
They'd made it, by at great cost. The Hanar faced extinction after the assault nearly wiped out their fleet, the Asari and Turians needed a new homeworld. Yet there was hope. Rannoch was still saved, as was the Krogan race, as was the rest of organic life as a whole. The friends and squadmates of Commander Shepard were free to live as they pleased.
The aftermath
Jacob moved in with Brynn and they were soon married. Their boy grew up to be a soldier, like his father before him. Jacob was indeed a better father that his own ever was, just as he'd sworn to both himself and Shepard. Jacob retired from private bodyguard work at the age of 43, making his money from the Cerberus Indoctrination Compensation Scheme. He was pardoned from imprisonment for his crimes as a Cerberus soldier due to his contributions to the Galaxy and in trial they found that he was truly only with Cerberus to fight the Collectors.
Javik didn't stay around for long after the war. He wanted to avoid becoming a museum piece and so he helped Doctor T'Soni with her books and her research, seeing it through until there were millions of copies spread across the Milky Way. Nobody would forget his people and the Reapers were slain. He had no purpose left. After he had secured his people's place in history, Javik disappeared. Nobody knows where he went. Many speculate that he went to his homeworld to end it all. Others say that he was hid in a bunker somewhere, trying to work out how to modify Collectors back into Protheans. All he told Shepard and T'Soni was that he wouldn't be back and that they shouldn't wait for him.
James Vega completed N7 training. He went on to have a long, fulfilling career in the Alliance Military, retiring from his position as Fleet Admiral at the age of 68. He married Doctor Michel who had served on his cruiser for several years beforehand. It took them 3 years of playful flirting before they went on a date, marriage took a further 5 years on top of that. They were happy together. James kept in contact with spectre Kaidan Alenko through his military career, the two of them became good friends indeed. When they could see each other anyway. Most of Kaidan's work was classified for obvious reasons. As they were too old to have their own child, James and Michel adopted an orphan from Earth. A little girl who they named after the Commander herself.
Jack continued teaching at Grissom Academy for many years following the end of the Reaper war. She used situations from the battles to stimulate and motivate her students. She eventually became head of the school, setting curriculums and new rules to ensure the safety and wellbeing of all students. Grissom Academy never again had a teacher as good for the students as Jack. She never allowed a child to feel alone or unwanted. She didn't retire until the grand old age of 120. Jack neither wanted nor needed a love life, that left her with more time to look after her students, who were (in her eyes) as much her children as any runt she could pop out. She lived until the age of 160. The person she kept in the most contact with was Miranda, surprisingly. Their banter let her keep her witty edge and Miranda always had Jack on her toes. When Jack learned that they were filming a documentary series for the ExtraNet about Shepard's feats, particularly the suicide mission against the Collectors, she was eager to help with script writing. There she reunited with Wrex, Garrus, Chakwas and Miranda. They would each have interviews that would be slotted in among filmed records of Shepard's exploits and animated recreations of tales that they told about her.
Miranda and Oriana lived on Illium with Shepard and Liara. Just a short walk away from each other's homes. Miranda aided Liara in her Shadow Broker work, taking calls from far away locations and buying Liara time to work on the million projects she'd taken on since the end of the Reaper war. Brokering information was right up Miranda's alley. It involved keeping a hold of contacts and learning everyone else's business, much like her time spent rebuilding Shepard. Miranda was the second person the filmmakers contacted when they planned making a documentary series about her life, which was understandable considering that MIranda was the woman who brought Shepard back from the dead. It was an impressive feat and it pleased Miranda greatly to know that she would receive recognition from her work at long last. Oriana met a man and raised a family with him. Miranda stuck to her work, as she always had.
Zaeed Massani retired. At last, he finally retired. He'd been through a lot in his time. Now he had all the time in the world all to himself. He moved to the new human settlement on Virmire (named Alliams after Gunnery Chief Ashley Williams who died on Virmire) to help colonists settle in, working as a labourer for anyone willing to pay. He worked construction most often, although butchering proved to be an easy job with his experience. Typically people left him to his own business.
Urdnot Grunt continued his life as a Krogan Battlemaster. He made regular visits to Commander Shepard and he was the father to many Krogan children. He named his first son Shepard, after the woman who saw him through his adolescence and the greatest warrior he'd ever had the honour to fight alongside. At least, that's what he told the press. He told Shepard that it was because the name seemed to come with blind luck. Unlike most Krogan, Grunt actually stuck around to look after his children and to teach them things about life, not just the battlefield. Grunt remained a warrior for the rest of his life, and never again would there be a fighter as great as the tank-bred ideal Krogan who learned everything he knew from Urdnot Wrex and Commander Shepard.
Kaidan served as a spectre for the 90 years following the Reaper war. During his time, he managed to completely wipe out the Blood Pack. The Council had never liked mercenaries, but they were all allowed to survive after the Reaper War on the condition that they stopped harassing people whilst in Citadel space. However, as Blood Pack continued to cause issues within Citadel space, the Council sent a team of three Spectres to wipe them out. Two spectres died on the journey but thanks to what he learned during his time aboard the Normandy, Kaidan Alenko survived with only one missing hand due to torture. When he finally retired, he returned to Vancouver to live out the rest of his years as peacefully as he could. He only kept in contact with Vega because the man wouldn't leave him alone. Kaidan liked solitude, and for the last years of his life he lived that dream. Every year anniversary of the end of the Reaper War, he'd send Commander Shepard a message to briefly catch up on how things had been with her.
Urdnot Wrex became the first Krogan member of the Citadel Council. He was as reasonable as Krogan ever got, and that was recognised by all. This allowed him to communicate effectively with other council races and progress the movements of the rapidly increasing Krogan population. The Krogan gained two new colonies on other planets to support their population and it wasn't too long before Tuchanka became a greater place to live again. Wrex supported the notion of having arenas for young Krogan males with too much violence in their hearts to fight in a controlled way. This allowed the Krogan to be more diplomatic and the first generation of genophage free Krogan were far more cooperative with other races. A memorial to Mordin Solus, the Salarian that ended the Genophage, was erected soon after the end of the Reaper War.
Karin Chakwas had seen war. After her experiences, any hospital would have been blessed to have her. But after the end of the Reaper War, she retired. She lived a long and happy life on Earth, running a small clinic where she would tend to the scraped knees of children and inspired them to be brave by telling them first hand stories of working with Commander Shepard. She kept in contact with everyone aboard the Normandy crew, particularly Shepard, Liara and Kaidan. Kaidan had become somewhat of a son to her over their time on the Normandy and so he received free healthcare for the rest of her working life. As much as settling down wasn't the life she had originally desired, a nice sit down was much appreciated.
Tali'Zorah lived on Rannoch. As much as she'd have liked to stay with Garrus to focus on the cleanup on Palaven, it wasn't possible and her people needed Admiral Tali'Zorah to help with the full recovery, although having the Geth around was very helpful. Tali became a vital part of the new Rannoch government and so she didn't have much time for personal matters. By the time she and Garrus finally reunited, they had both agreed that their relationship was too spontaneous and focused on the fact that it may have been their last opportunity to find love before the end. She ended up becoming the partner of Captain Kal'Reegar, and they had two children as their contribution to the repopulation of Rannoch. She did keep in contact with Shepard, the two had become good friends over the years and Tali was probably more loyal to Shepard than to her own people. She saw the first generation of Quarian children without suits be raised on Rannoch and it was for that reason that she lived out the rest of her days happily, knowing that she had contributed to all of this gain.
EDI was immortal, as long as she could maintain the functioning of the body that she inhabited. Joker was not. Still, the two pursued their relationship and were soon married. They adopted a Krogan child whose father died and whose mother couldn't afford to feed it. Joker didn't have a great deal of involvement in raising the child because of his Krolik Syndrome, but he was still a remarkable father and the child was helped through adolescence by Aunt Shepard and Uncle Grunt. The two lived on the Citadel after retiring from the Alliance since it had the best medical care for Joker that they could find. He lived until the age of 57 when his ribs gave out and crushed his internal organs past the point of recovery. His funeral was small; only Shepard, Liara (and baby), EDI, Garrus and Tali were present as his family had all died following the Reaper attack on Tiptree. EDI continued to serve the Alliance after Joker's death. She never went rogue.
Garrus Vakarian. The Hero from Palaven. Archangel. General. Garrus went on through the ranks of the Turian hierarchy and whilst he may not have made Primarch, he did himself and Shepard proud. He met with his best friend regularly at Purgatory on the Citadel, and later when they couldn't handle the noise so much they relaxed at Eternity on Illium. The two reminisced and exchanged stories and remained the closest of friends for the rest of their lives. After all, there's no Shepard without Vakarian. Garrus received the honoured position of Godfather to Shepard's child alongside Feron and Tali was awarded Godmother. He joked that it was more difficult a job than working at C Sec. Garrus found a partner on Palaven and together they had 3 children, one of which was given Shepard's first name. Garrus received many bonuses for interviews and received royalties on vids about his and Shepard's exploits. He was accredited with the highest honours a Turian could receive yet he still retired fairly late on in his life. Garrus needed to keep himself busy and there was never a shortage of things to do on post-war Palaven. He was offered the position of Turian councillor, but politely declined, knowing that a life of politics was definitely not for him.
Liara T'Soni continued her information brokering for 860 years before finding someone else to take over her empire, with that person being her daughter. She didn't really keep in contact with anyone other than Garrus and Miranda (and obviously Shepard). Little Ilyssa took up most of her time outside of work. The war had taken its toll still. Sometimes she'd have to roam around Illium late at night looking for Shepard who had wandered off in some kind of drunken state. They hid the PTSD and the scars they bore from their daughter well and the only way that people knew that Shepard was her biological father was from her name on the register. The Parent-Teacher meetings were fun too. What teacher would dare tell Commander Shepard that her daughter was boisterous? Not many. Liara fought hard for Ilyssa to not join the military. So when she found her with the Eclipse sisters Liara lost her temper completely. That was when she told their daughter that Shepard had killed for the first time. Of course, their daughter knew Shepard had killed Eclipse mercenaries before. It was an accepted part of life. But that was the first time that it had really sunk in. After Shepard's death, Liara got into contact with Wrex and the two of them became very close friends. Eventually, when Liara reached the Matriarchal stage of her life, she became a teacher. And her stories never failed to amuse.
Shepard retired immediately. With all of the royalties from advertisements and vids and documentaries, she never had to work again. She spent her time catching up with Garrus, visiting the Citadel to kick the council up the ass, helping Joker and EDI out with their little girl, teaching Grunt's son called Shep how to headbutt like a true Shepard and of course, raising the daughter of herself and Liara. It was incredible how in spite of them being of a different species, their daughter was a perfect mix of them. Shepard's stubbornness with Liara's intelligence made for a brutal opponent when it came to bedtime. Shepard was free to live as she liked and she only had to make it through 29 assassination attempts after her retirement. Of course, there was a downside to having too much time alone and out of employment. Shepard drank. A lot. She hid it from her daughter but she couldn't hide it from the Asari who came after her about half an hour later with a blanket and a sympathetic look in her eye. Nobody could ever come close to going through what Liara and Shepard had gone through. Yet they used that bond to grow stronger, and Stars know that there was never a greater parenting team than Commander Shepard and Dr Liara T'Soni. Shepard lived for an extraordinarily long time due to her cybernetic implants (hell, she even outlived Garrus), but it was nowhere close to how long Liara and their daughter lived for. Shepard was the most decorated War Hero in history.
Shepard defeated the Reaper Indoctrination
Shepard's crew defeated the Reapers
They lived long, happy lives in the safest Galaxy that anyone had seen for billions of years, with no threat of Reapers.
Player Victory!