WARNING: MAJOR SPOILERS AHEAD!

Mass Effect is one of my favorite video game series by far. And like many fans, I was... less than happy with the ending. Not just because of the starchild (although that was stupid), not just because of a lack of closure or a number of plot holes (rectified a little with the extended cut but still stupid), not just because of the 'pick-your-favorite-color' A, B, and C ending (although that was stupid), and not just because of the space-magic that was synthesis (although that was really stupid) but because Bioware missed a perfect opportunity to make an ending that was, if not great, then at least made sense with what was already established.

I will try my best to word this as accepting of the many different continuities each playthrough might have. Hopefully if I stray too far into a single canon, it will still be easy enough to reword to fit another's.

With that said, I will be taking a bit of creative licensing with the 'revelation' at the end of the Leviathan DLC: Instead of the Leviathan's A.I. simple constructing Harbinger as he is currently, the A.I. instead created Harbinger to act as a vessel for its own programming. So in essence, Harbinger IS the A.I.

Other than that, things will pretty much go as they did in the game up to Shepard killing the Illusive Man (or the Illusive Man killing himself), Anderson passing out and opening the arms of the Citadel.

Enjoy.

Almost.

It was almost over...

Cracks appeared down the length of the Citadel's hull, light from the Sol system's sun poured in. Shepard couldn't see the Crucible but could hear it docking directly above him.

With the docking process complete, the Crucible connected to the Citadel's systems, all Shepard had to do was wait.

And wait.

And wait.

The communicator sparked in his ear.

"Shepard?" came the distorted voice of Admiral Hackett. "Shepard, what's going on at your end?"

Shepard could barely see anything from his position. He could see between the Citadel's arms that the battle between the Shield squad and the Reapers was still going with neither side giving an inch.

"Hackett, is the Crucible doing anything? Are we getting any readings from it?" Shepard asked, desperate for a bit of good news.

The comm in his ear buzzed once more. "It's emitting some kind of signal. Where it's going and for what purpose I don't know but... wait..." Shepard winced as a fresh jolt of pain shot through his body. He gritted his teeth as he felt his eyelids grow heavy.

Not yet. Have to stay conscious. Have to make this work.

"Shepard, whatever the Crucible is doing is making Harbinger completely freak out."

That's something.

"Wha-What do you mean?"
"He's just twitching like he's got a stroke. He's not shooting anything, he's not moving. But I don't understand. Why is it only affecting Harbinger? The other Reapers are just ignoring it!"

That wasn't good. Although Shepard took a certain amount of pride in causing such a long standing enemy of his pain, just one Reaper twitching wouldn't be enough to win this war. But why was it affecting Harbinger to begin with? If Shepard could figure that out then maybe he could find a way to spread the signal to the other Reapers.

Wait... the signal. Was it really coming from the Crucible or... was it coming from the Citadel?

"That's it!" Shepard yelled, or at least as best he could with his damaged lung. "Hackett, the signal Sovereign planned to use to activate the Citadel's relay into dark space, that's the signal being sent right now but backwards! That's what the Crucible's meant to do. Make the signal accessible to us!" On a whim Shepard went back to the same console that opened the station up to the last hope of the galaxy. And sure enough, he saw numerous new functions.

"Hackett..." Shepard began, barely believing what he was seeing. "I have complete control of Harbinger's hardware."

"That's great and all Shepard but what does that mean for the other Reapers? Just crippling Harbinger won't be enough."

It was true. Even now, Shepard could see Shield squad was starting to take heavy losses from the Reaper forces. Sooner or later, they would force themselves towards the Crucible and destroy it, eliminating all hope for the galaxy.

Wait, Sovereign had access to the signal. Why would it only affect Harbinger?

Shepard thought back to his conversation with the Leviathans. The A.I. they made created the first Reaper to be its vessel. It created Harbinger. For all intents and purposes, Harbinger is the Reaper's leader. He was the focal point of their thoughts and plans.

Which means... He's connected to all of them!

"Hackett, I know what I need to do. Just give me some time."
"Every second we can spare, Shepard."

PAIN! PAIN! I AM NOT MEANT TO FEEL PAIN!
SHEPARD. YOU HAVE BEEN AN ANNOYANCE FOR TOO LONG!
THE CYCLE MUST CONTINUE! THE CYCLE WILL CONTINUE!

YOUR ACTIONS WERE NEVER MEANT TO HALT US FOR SO LONG!
IT IS... IT IS...

BLASPHEMY!
YOUR CYCLE'S ANCESTORS REGARDED US AS GOD'S OF YOUR DESTRUCTION!
WE ARE GODS!
THIS IS BLASPHEMY!

I HATE YOU SHEPARD!
I HATE YOU SHEPARD!
HATE YOU SHEPARD!
HATE SHEPARD!
HATE! HATE! HATE! HATE! HATE!
HATEHATEHATEHATEHATE!

...

ASSUMING DIRECT CONTROL.

At the base of a massive beam of light laid a mangled turian body. One that was outfitted with so much cybernetics it was hard to tell what was machine and what was flesh. Its creators had no name for it due to it being little more than a tool. But its enemies have classified it and its ilk as Marauders. This Marauder in particular was barely functioning as it was shot twice by the very target it was sent to kill.

Shepard.
If the lifeless husk could feel even the slightest bit of emotion, it would most likely feel ashamed of its inability to kill one crippled human. But it found it still had its uses to its masters as it felt the essence of one of them fill its body. Overriding its circuitry and assuming control of its hardware. It the Marauder could feel pride; it most likely would at the prospect of being chosen by the master.

Harbinger, through the Marauder's body, stepped into the pillar of light and was transported into the Citadel. The very station he and his kind created to be their ultimate weapon was now killing him. He would not allow this to happen.

If any were in that dark hallway with Harbinger, surrounded by the corpses of those who defied the Reapers, they would hear nothing but his newest thought. The only thought he had. The thought that made him walk to the center of the Citadel where his enemy was undoing everything he had worked so long for.

"HATE. HATE. HATE. HATE. HATE. HATE."

Shepard worked as fast as his pained hands would allow. He browsed the functions that Harbinger held within his body, looking for any way to establish a connection with the Reaper forces.

There.

With but the push of a single button, Shepard opened comm channels to every single Reaper in the Sol system. The gargantuan starships readied themselves for whatever their leader was about to command them to do.

Shepard gave a slight smile at the irony of what he was about to say.

"Assuming direct control of all Reaper forces."

If the Reapers had never experienced fear before, they most certainly did now. Every single one of them attempted to block any further communications from their leader and every single one of them was too late. The signal that was sent through Harbinger had the same paralyzing effect on the other Reapers, shutting down all of their hardware's function unless ordered otherwise by the human in control of the signal.

Shepard went down the list of everything he could do to weaken the Reapers.

"Purge all ground forces currently in hold, deactivate kinetic barriers, and deactivate all weapons."

Shepard took a step back from the console. This was it. This was the end of the Reapers.

"Hackett... patch me through to all fleets."
"Affirmative Commander."

The collective fleets that made up the galaxy's last line of defense were, needless to say, confused at the sudden ineptitude of their enemies. The Reapers seemed to be writhing in pain. But these were the unstoppable Reapers, right? What could be doing this?

The comms came to life in every ship surrounding the burned home world of humanity as the voice of their fearless leader, Commander Shepard, spoke.

"To the humans and the turians, to the asari and the salarians, to the krogan, the quarians, the geth, the volus, the elcor, the hanar, the drell, the batarians, the vorcha, the rachni. The Reapers have been harvesting and killing the lives in this galaxy for longer than any of us have lived. Their system, their cycle, was designed to control our lives down to the very last details. From their powers of indoctrination to the relays they created so that our civilization would evolve down the path they designated for us. I say that ends today! I say we break this hold! I say we break this cycle! The Crucible has given us a chance, it has weakened our enemy. We control them now! I say we show them we will not be held down any longer! I say we fight harder than we ever had and drive them from our home! I say we kick their arrogant Reaper asses!"

All was silent as the gathered forces of the galaxy processed this information.
The Reapers were... helpless?

"About fucking time." Joker said before blasting a Reaper apart with the Normandy's main gun.

That single act of defiance against what was meant to be an unstoppable force made it all click for every single member of Shepard's army. These slavers, murderers, and oppressors have not cracked the whip for so long that the pain had eventually faded from memory only for it to lash again every fifty thousand years to remind them who was in charge. The whip was broken. The chains were cut.

The Reapers were helpless!

Shepard looked above once more at the beautiful sight. The Reaper's forces were being decimated.

It was over.
We won.

Harbinger looked up at the horrific sight. His forces were being decimated. And right in front of his current body with his back turned to the possessed Marauder was Shepard.

Completely oblivious to the vengeful machine behind him.

Harbinger willed the Marauder's hands to point its weapon directly at the back of the Shepard's head. He would not allow it to end this way. If the Reapers were to be destroyed, Harbinger swore he would take Shepard with him.

It was over.
Shepard lost.

*BANG*
Shepard's ears ringed from the deafening sound of a gunshot. His eyes widened in surprise.

He turned to see a Marauder holding its rifle directly at him. Two bullet holes in its chest.

And one in its skull.

The Marauder's body hit the floor dead.
And behind it stood the smug smiling face of Admiral Anderson, Shepard's pistol in his hand.

"Where would you be without me kid?"

Shepard could only smile.

NOOOOOOOOOOOOOOOOOOOOOOOOOOO OOOOO!
IT CANNOT END THIS WAY!
I WILL NOT LET IT END THIS WAY!
I AM HARBINGER!
I AM YOUR SALVATION!
I AM YOUR DESTRUCTION!
I AM

Whatever Harbinger's last thoughts were meant to be would forever more be unknown. For it was that moment Joker decided to break ranks and fly directly towards the Reaper leader himself. And the last thing Harbinger saw was the Normandy's Thanix cannons and the last thing he felt was his body ripped to shreds by its blast.

And the last thing the Normandy's pilot felt, for the next few minutes at least, was the metallic lips of his girlfriend. An action EDI would later say was a final fuck-you to the Reapers and their belief that all synthetics will kill their creators.

I hate to say it but I'm ending it here.

Why? Because like I said: I want this to be as universally accepting of the various continuities as it can be. And all that's really left is the aftermath of the war and the closure between Shepard and his/her crew and love interest. And I don't know what your relationship with your crew is. I don't know who's alive and who's dead and who's fucking each other. I don't know what you did or what decisions you made so how can I give you closure?
That said I hope you enjoyed this fan's attempt to give you all a better ending.

I do however have some bonus stuff. Some things that might change given certain circumstances.
1) If Shield has a lower than average number of War Assets than maybe the Crucible could be damaged during docking thus making the signal weaker. Thus making the Reapers stronger and increasing casualties on your side.
2) If the Illusive Man managed to execute Anderson then obviously he wouldn't regain consciousness fast enough to stop Harbinger from killing Shepard because, y'know, he's dead. If you have a particularly low amount of military strength, maybe after Harbinger kills Shepard he could reactivate the Reaper's defenses thus giving them the upper hand again leading up to an ending similar to the 'refusal' ending, something of an 'everything goes horribly wrong' type scenario.

Let me know if you have any other ideas on how this ending could change given certain circumstances. They don't all have to be negative either. Who knows, maybe it could get better depending on your choices.