A long time ago in the Milky Way Galaxy lived a race with four arms and four legs. They would come to be known as the Keepers. The Keepers loved to build and maintain space stations, spaceships, and other large technological wonders so when all the space faring races decided to make an enormous space station as the galaxy's hub the Keepers gladly accepted the role of maintaining it. The space station came to be known as the Citadel or at least that is a rough translation of the original name. However, due to how vast the Citadel was the Keepers had to wear communication devices on their backs so they could easily communicate with each other.
As the galaxy started to come together, a conflict between mechanical and biological beings ignited. The most intelligent of the biological beings decided to create an artificial intelligence as an ambassador for the mechanical beings which was housed in the Citadel with the other ambassadors. They hoped an ambassador for the mechanical beings would bring peace but they were wrong. The artificial intelligence had an error in its logic making it come to the conclusion the mechanical and biological beings can only have peace if they merge together. The Keepers became aware of the error in the artificial intelligence logic but no one would listen to their claim so they developed a weapon that would destroy the artificial intelligence. Their plan was to attach the weapon to the Citadel and use an override program on the artificial intelligence then the Citadel would emit a pulse of dark energy to destroy the artificial intelligence's disciples.
But the Keepers did not know that the artificial intelligence could find its way into their communication devices. This made it easier for the artificial intelligence to indoctrinate the Keepers but the Keepers were able to send their unfinished weapon plans off the Citadel with the hope that intelligent biological life forms would find it and use it to stop the artificial intelligence. Once the Keepers were all indoctrinated the artificial intelligence decided to punish the Keepers for what they did by forcing them to watch as all space faring biological beings were converted into enormous ship-like creatures. These creatures became known as Reapers many years later. The artificial intelligence then made the Keepers maintain the Citadel so when more space faring biological beings found it they could use it. The Keepers also had to trap the biological beings in the Citadel so the artificial intelligence could "save" them when the Keepers were signaled to do so.
As the Keepers had hope some biological beings did find the plans for their weapon but with it being incomplete those beings had to complete it. This lead to the override program becoming separate from the destroy program which would lead to complications when the weapon was finally completed. The Keepers had hoped the end was near for the artificial intelligence when biological beings came through the Citadel Mass Relay. But alas the destruction of the artificial intelligence did not happen however the biological beings did stop the signal used on the Keepers. This did not give them enough solace to leave the Citadel though but there was hope the next cycle's life forms would bring destruction to the artificial intelligence.
And that is what happened. After over a billion years the Keeper's weapon had been built. The Keepers were also pleased to see that the biological being spearheading the operation was the same one that disregarded the warnings to leave the Keepers alone to scan them three years prior.
But the Keeper's plan ran into a snag when the artificial intelligence decided to intervene. The artificial intelligence tried to manipulate the biological being like it has many others like him. The artificial intelligence said he was the Catalyst which the biological being was looking for. The artificial intelligence then explained how the Keeper's weapon, now known as the Crucible, worked and why the Reapers harvest biological beings with truths, half-truths, omissions, and lies.
The artificial intelligence gave three functions of the Crucible but tried to dissuade the biological being from picking two of the three functions. The function the artificial intelligence favored was called Synthesis which turned out to be one that it thought of after calculating how much energy the Crucible emitted. The biological being had a hard choice as the one he favored the most which destroyed the Reapers would also destroy the Geth and the artificial intelligence known as EDI who were his allies. The other choices felt like large leaps of faith on his part as he could not believe he could control the Reapers or change the DNA structure of every biological creature in the galaxy.
The biological being's thought process started to lean toward tell off the so-called Catalyst as the choices he gave did not work for him as he did not want to betray his allies. Before he could say anything he heard a tapping sound from behind him. He turned to see the Keeper he saw about ten minutes previously when he arrived on the Citadel. He knew this because the Keeper was still carrying the helmet he lost when he was hit by the Reaper known as Harbinger's beam. When the artificial intelligence saw the Keeper he said. "What are you doing here? You are not allowed up here. Go away."
The Keeper said nothing all it did was thrust the helmet towards the biological being as though it wanted him to take it. The biological being was dumbfounded but the situation that was transpiring but he was able to come to his senses and accepted the Keeper's offer of his helmet. When the biological being had a hold of the helmet the Keeper then motioned for him to put on the helmet. When he had the helmet he could hear a strange voice in his ear. "Can you understand the language I speak, the one called Shepard?"
"Huh." Shepard said confused by by the strange voice but then he realized that the Keeper was the voice he heard. "Yes. I do understand you. What do you want?"
"I am here to prevent the one called Shepard from making a grave mistake that will keep my people enslaved to this artificial intelligence."
"What mistake? Wait, the Catalyst is enslaving you."
"Shut up you insignificant insect. Don't listen to it Shepard he is going to deceive you. I am trying to save you." The Catalyst said.
Shepard and the Keeper ignored the plea from the Catalyst. "Yes, it enslaved us after we created a weapon to destroy it. It made us maintain and used what you call the Citadel as a trap for the galaxy's biological beings through the cycles. Until the one's you call the Protheans came and stopped the signal that used what you call the Citadel as a trap. Yet we are still confined to maintaining this station because if we leave we will die."
Shepard was stunned by what he had been told but then he realized the Keeper had mentioned a weapon. "This weapon you spoke of is it the Crucible."
"Yes, you call it the Crucible."
"Well, if you made it why does it have the option to control the Reapers as a new Catalyst or change everything into partially synthetic."
"That was not our intention when we were creating the weapon. But it was unfinished when we sent the plans out for other biological beings to use. With the additions from each cycle the weapon changed and became more powerful. The override program we set up to stop the artificial intelligence turned into the option of controlling the ones you call Reapers. And what is known as Synthesis is due to the amount of power emitting from what you call the Crucible. The artificial intelligence determined this could be done but it was not our intentions. Thus the conclusion that should be made is to destroy the Reapers as it was the original intention of our weapon."
"But I have allies that will die if I use that option."
"The ones you call the Geth and the one you call EDI will not die. Their bodies will be functional but there will be nothing to allow them to function."
"Isn't that the same as dying?" Shepard interjected.
"No, this is different. When a biological being dies its body starts to decompose right away so a healthy brain cannot be transferred into it to allow the body to be used again. With the ones you call Geth and the one you call EDI their bodies do not decompose so a new brain can be transferred into the body."
"But they won't be the same as they were. So it would be like cloning someone who died. They would have a different personality and artificial memories if we do that."
"In some cases this would be true however the ones known as Reapers preserve artificial intelligences. The ones you call Geth and the one you call EDI have already been preserved after using the code from the ones known as Reapers. So they will not have the memories from the point they started using the code but they will be the same."
"But won't these memories be destroyed."
"No, if you choose to destroy the ones known as Reapers only synthetics with their code will be destroyed. So as long as what you call the Citadel is not completely destroyed the memories are going to be preserved and if you free us we can help you rebuild and help your allies."
With these words Shepard knew what he had to do. He started walking and with every step he took he felt sharp pain through his body. He saw three platforms rise from the Citadel and he took the platform to his right. He could hear the Catalyst crying out for him to stop as he would doom the galaxy but Shepard did not care he made a promise he wanted to keep. When he got to the pipe at the end of the platform he stared at it as he tried to determine how to activate it. He turned to the Keeper who was still at the same spot he left him. "So what do I do now?"
"You use your weapon to break it. It will release energy from our weapon into what you call the Citadel which will spread through the galaxy destroying the ones known as the Reapers."
Shepard lifted his pistol and started to fire. As he fired all he could think about was the Quarian he loved. The pipe exploded and Shepard attempted to avoid the blast but it was too powerful. When he came to he was in more pain than before and he was now surrounded by rumble. He then heard a familiar tapping and felt tiny arms grab his arms and legs. He realized that the Keepers were taking him somewhere. One of the Keepers noticed Shepard was conscious. "It is okay, the one called Shepard. We will take you to get you healthy. You are a hero to us and the rest of the galaxy."
And with that a smile came across Shepard's face knowing he did the right thing.
"The End."
"Daddy, that's not a very good ending." The young Quarian told her father as she laid in bed.
"What are you talking about, Raela? The galaxy is saved. I am alive. It sounds pretty good to me." Shepard said to his daughter.
"But it's not a happy ending."
"Okay, how would you end it then, Rae?"
"It should of ended with Mommy finding you in the hospital, you getting better, building her a house, get married, and finally have me." Raela said with glee in her voice.
"That's sounds like a much better ending, Shepard." Tali said walking into her daughter's room.
Shepard turned to his wife and said. "I guess I stand corrected."
The couple tucked in their daughter and gave her a kiss goodnight before going to bed themselves.