So this is my take on the game and how it could have went in the end.
Something Bioware didn't use that would've been a great way to tie the Prothean artifacts and Javik into the game.
This could've been another option for the game.

Also this is AU and will have flashbacks of different parts of the three games. It mostly will be of what happened after.
It will also have some moments before the game dealing with Shepard's life before joining the Alliance.

It has violence, sex, foul language, and MATURE CONTENT.
Also if Yuri , Femslash is not your cup of tea then you SHOULD NOT READ ANY FURTHER!
Also no beta so all mistakes are mine. And of course Bioware owns Mass Effect 1,2,3, story,.. Except for what I've added as extra.

Chapter 1::…

If I stop today it was still worth it. (From Gia Carangi )

_-_-Start flashback Javik _-_

He stood there waiting for Shepard to leave. Giving her time to escape. He was going over everything the starchild said and looking at the choices before him.
Shepard looked at him one last time and put her hand on his shoulder to convey what she was feeling through the touch sensory he has.
It was easier this way then to try to speak.

That single act spoke volumes and he was grateful for the last contact. Then when Shepard was sure, she turned and made her way to the exit leaving him behind.
As she left part of her felt guilt and another felt pride. She knew that he could feel it also.

So here he was on the Citadel but a very different part of the thing that was once the heart of his people's civilization and that had falling long before he was born.
He found himself asking questions he knew would never have an answer.

Was this part of the Citadel always here or is it something more recent?

If new then why did this cycle not know about it? Or did they just hide it away for fear of what it was?
So many questions unanswered or never asked in the first place.

Yet he also found himself asking if it was always here why his people never used it.
Maybe this was the part that never got finished in time.

Everything was certain to him up until this point. Now the fate of all living species fell on his shoulders. The price was bigger then what was originally set before him.
He couldn't falter now not so close to the end of his mission.

He waited for what felt like hours to make sure Shepard was gone before he made is choice. Knowing that no matter his choice one has to be made even if that choice was to do nothing and allow them to fight to the end of their very existence. It was still a choice. One he wouldn't take lightly.

He considered his options and what the starchild had said. What his people had endured and also what Shepard had accomplished. What this cycle had shown him.
Many things fluttered through his mind as he took everything in.

He knew that he could choose to let the fate play out and see if this fight would hand victory to them or the Reapers.
That was something he found himself a bit amused about because he knew it would only end one way and that way favored the Reapers. That thought was dismissed.

He knew that destruction of the Reapers was what his people would of done.
However while serving with Commander Shepard and seeing first hand that there was more out there and that he was left with two very different options besides Destroy.

Control or Synthesis.

Javik knew there was no way he was becoming a Reaper even if it meant having control. He knew that it also didn't mean he would truly have full control because that was proven by the starchild.

Synthesis however would bring the two together as one. However that would be forcing a decision on everyone and it was no different then what the Reapers was doing but it would bring peace ,.., or would it.

He knew what his people would do but, he now asked what would Shepard of done. In that moment he found clarity and chose the same thing. Destroy them not because it was what his people would do but also what Shepard would do knowing that the Geth and EDI would in a sense die. It also gave all life the chance to change and choose their own path. It was what they were fighting for anyways.

So he made his way to the destroy option. Flashes of his people with glimpse of pride on their face played before him. Then came the flashes of his time aboard the Normandy and the last one of Shepard with a smirk and a nod of approval. Then everything went black as the force of the explosion hit him.

_-_-End flashback_-_

The last thing Commander Shepard remembered before the calm took her was a warm blast of red light washing over her and she felt a crushing weight. When she was able to take in a breath the fiery pain swept through her. She didn't know how long she was knocked out.

She didn't know where she was. She started to remember things. The battle for Earth and the Reapers. She tried to focus on her surroundings but everything was black. She could taste dirt and metallic debris. Everything hurt and burned. The throbbing in her head was loud. She could only move her head. That in itself hurt and caused more pain.

She had to get help and she knew that if anyone was alive that finding her would be beyond a miracle.

She started calling for help. Then hours later her voice gave and she had to find another way. She was able to feel a medal pipe next to her left hand. She managed to move her hand and grab the pipe just enough to bang it against another piece of medal to start sending out an SOS.

It had taken three days for them to find Commander Shepard amongst the rubble. She was barely noticeable. Hallucinations were already sitting in. The rescue team was able to get her to one of the military makeshift hospitals in a ruined building not far from the original assault took place.

The medical team worked on her for several hours. It was touch and go several times. Someone was finally able to locate Miranda Lawson three days later. She was able to arrive at the location three days from the time they contacted her. Once Miranda was able to keep Shepard stable they were able to move her to better felicities.

It was more then a three weeks before Shepard was awake again. She had suffered sever injuries to many organs and her cybernetic that Cerberus had implanted was causing problems. With Miranda's knowledge they were able to keep Shepard alive and on the path to healing.

Now it was four months later.

Shepard was move to an apartment with Miranda and her sister Oriana. This was mainly for medical reasons and so Shepard could be around familiar people while she healed. Miranda had set up a room for her in the study that was going to be Miranda's office. Shepard was healing nicely with only a few complications with her ribs.

Now two weeks later and she was doing much better.

Taking Miranda's advice. However that could be due to the fact that Oriana was left home when Miranda had business to take care of. Today was no different and she was in her room while Oriana was making dinner.

She had on a gray tank top and her baggy cargo camo shorts along with her N7 hoodie and a pair of socks. She was stretched out on the couch. One leg stretched out with the other bent at the knee.

She had a datapad in one hand and the other was holding her Scotch. She knew that she shouldn't be drinking. Not with the medicine she was on for her four broken ribs and the torn ligaments in her right shoulder. The pain was not going away and it was hard to sleep.

She was thinking about what had happened during the last push for Earth. She was at the last stages of healing from the fall she took leaving the Citadel. Some of the pain she felt was guilt because she was the one who should of made the choice not Javik. Somehow in the mist of it all he managed to find his way to her and to the starchild.

To make the decision of how to deal with the Reapers. He pleaded and begged her to leave. He wanted no ,.., needed to be the one. To set things right. He was the last of his kind that they knew of and he had a mission to finish that was so long in the making. She understood this and with a heavy heart left.

A knock on her door and Oriana voice startled her out of her thoughts.

'Come in'
said Shepard as she sat the glass of Scotch down and out of sight.

'Um ,.., I hope I didn't disturb you Commander Shepard,but dinner is almost done. Also Miranda will be home late.'
Oriana said with her usual quite tone.

Shepard looked at her and was slightly sad that Oriana still insisted on calling her Commander Shepard.

'Oriana please you don't have to call me Commander Shepard. No one does anymore. Just call me Marz.'
Shepard was taken back by the sound of her given name. It had been so long that anyone had said it that it seemed foreign coming out of her own mouth.

That very line she just spoke was not so different from what she said to James Vega moments before the Reapers hit Earth.

_-Flashback_- James ''Commander''

Shepard "Your not suppose to call me that anymore, James''

_-End Flashback_-

Of course most of the time people just called her Shepard. So to many that was her name. Even to her it was like "Shepard" had replaced most of who she was. She was pulled from that thought once again at the sound of Oriana voice.

'Ok, I'll try to remember that. Oh,,.. before I forget. We have had word that the Normandy has been spotted and should be in Earths orbit in the next twelve hours.'

As Oriana spoke she was not sure if she should of said anything concerning the Normandy.

Considering the fact that Shepard hadn't spoken of anything concerning the war or the aftermath of it. But when she looked at Shepard face she seen a bit of hope.

Shepard tried to keep her composure. She looked to Oriana and with a nod and a slight grin.

'Thank you Oriana. I'll be there in a moment.'

With that Oriana left and went to finish dinner.

All kinds of things went through Shepard mind as she went to put away her Scotch and the datapad she had been looking at. Could the news be true. If so was the crew alive and if so what state would they be in. It had been close to six months from the last time she seen any of the remaining crew that left on the Normandy.

She had a few moments during her initial stages of healing that her memory of people and some places was lost in the mist of it. In other words she had lost some of her memory for a short period of time and had some bouts of memory loss up till lately. It was something everyone had expected to happen due to the damage her brain had sustained.

A few moments later she was at the table with Oriana. Halfway through dinner Miranda made it home. Miranda looked exhausted. She took a job at the local clinic to help with the many solders that needed help that only someone like Miranda could give. With her research and work on the Lazarus project she was the best they had.

Miranda was quiet during dinner and into the later half of the night. She looked like she was lost in thought. Oriana tried to talk to Miranda while they were cleaning up after dinner, but was only met with cold replies from Miranda and finally told drop it and leave her alone. This caused Oriana to storm off to her own bedroom and slam the door to her room. Miranda finished cleaning up and then went into her own room. Shepard over heard and seen some of it play out while trying to make her way back to her own room.

Once inside her own room Shepard got comfy on the bed with another datapad and the remainder of her Scotch. These next few hours were going to already be hard for her to go to sleep and with the anxiety of knowing that the Normandy was making its way back to earth would not help her sleep if she got sleep at all.