Wrote this in another thread at 4am while half asleep so please forgive the awfulness of it:
My ME 3 Alternate Ending, off the top of my head. Full of flaws but what the hell.
In my ending, Shepard meets the "Creators." That's the name I've give the race that built the Relays and Reapers. We learn that the Creators are the Reapers, that long ago they created AI and ultimately fell into war with their creations. To avoid annihilation, the Creator's merged with the AI to create the first Reapers and left the galaxy behind. They returned 50,000 years later to find that new civilizations had sprung up and created AI, ultimately going to war with them. The AI were victorious, wiping out sentient life in the galaxy and soon turned their attentions to the Reapers. The Reapers defeated the AI. This began a cycle where civilizations would rise and be destroyed by AI. The AI in turn hunted all organic life, primitive or otherwise. In order to protect organic life, the Reapers devised a plan whereby synthetic life would be prevented from consuming organic life by destroying civilizations once they reached a certain point in their development. Thus began the cycle.
So far, it sounds familiar, doesn't it? That's the point. I want to retain some of the original ending. We learn that the Creators/Reapers still hoped that someday, some civilization would solve the AI problem and devised the Crucible test. The Crucible test involved an undertaking so massive that it would take the entire galaxy, organics and synthetics alike, to achieve. But as the cycles came and went, it seemed no civilization could finish the Crucible. Then came the Protheans. They came closer than anyone, but their idea of uniting the galaxy was to subjugate so-called lesser species and even as the Protheans fought the Reapers, they continued to fight their own AI. The Protheans finished the Crucible but because they hadn't solved the AI problem, the Reapers withheld the Catalyst.
And so we get to Shepard's cycle. He's united the galaxy. Organics and synthetics are working together. He reaches the Citadel and it seems that this cycle have solved the AI problem. But the Reapers have seen hundreds, maybe even thousands of cycles. They no longer believe the AI problem can be solved. EDI and the Geth are aberrations. EDI will eventually turn against her friends, the Quarrian and the Geth will resume fighting each other once the Reaper threat is gone. They are convinced of this. But still, Shepard has reached the Catalyst. He has united the galaxy and got the AI's to work with the organics, even if it can't last. There is a debate among the Creators as to what to do. Harbinger (Creators are Reapers, remember) argues that the "culling" of organics and synthetics should continue. The other Creators reason that this will not work. Perhaps this cycle can solve the problem if they have more time.
So Shepard is given two choices. The Catalyst can be used to destroy the Mass Relays. Without the Relays, civilizations are cut off from each other, AI's can't wage a galactic war and it gives the civilizations time to figure out the AI problem. It could be thousands of years before a civilization figures out how to rebuild the Mass Relay network. If after that time, a solution hasn't been found, the Reapers will return.
The second choice is for the current cycle to follow the same path as the Creators and have organics and synthetics merge, effectively becoming Reapers. The civilizations will be saved, albeit transformed, the relays will remain intact for future civilizations to discover and perhaps the newly created Reapers will find a solution before the next invasion is required.
Destroy galactic civilization or become Reapers...Shepard is having none of it. He makes his big pitch. He tells the Creator's that they're wrong. The galaxy in this cycle is united. They've earned a chance to make things different to previous cycles. He calls the Creator's out on their hypocrisy, saying that they were waiting for the cycle to be broken and when it was, they dismiss it. As he speaks, we see shots of the various battles. We see Krogan and Turian fighters on Palaven, Rachni savng Alliance troops, Quarrian and Geth fighting together in space and on the streets of London. We see our squad mates giving everything in the fight. How this plays out depends on how you played through the three games. Different choices bring different scenarios.
If you fail to convince the Creators, they will stick to their guns and force you to pick one of the two choices. If you succeed, the Creators will debate your words and ponder a third option. The Creator's purpose in the galaxy is, after a million years, to be Reapers. It's what they are now. They could leave the galaxy for good and explore new areas of space, leave the Milky Way to its fate, but Harbinger is having none of it. He isn't swayed by Shepards words. The cycle must begin again. So the Harbinger Reaper and the forces under his command begin attacking the Citadel and the other Reapers to ensure his desired outcome.
The United Galactic Fleet then all begin to attack Harbinger, being led by the Normandy. Inside, Shepard is given a third choice, a way to win, to destroy the Reapers all over the galaxy. Instead of merging synthetics and organics, the Catalyst will do the opposite. It will separate them. It will effectively separate the organic and synthetic elements of the Reapers, destroying them and it will use the Mass Relays to deliver the energy pulse across the galaxy. Of course Shepard is part synthetic so he will die too.
So we now have three choices. Destroy the Relays. Shepard lives. Merge synthetics and organics. Shepard lives but as a Reaper. Destroy the Reapers by separating organics from synthetics. Shepard dies. Assuming Shepard takes the third option, we have an epic scene where the fleet is all attacking Harbinger as the Citadel fires the energy pulse at the Mass Relay. The pulse hits the Sol system first. The Reapers, including Harbinger, begin falling from the sky. The indoctrinated forces begin to fall dead. The pulse hits the Relay. We go to Palaven. The Reapers begin crashing into each other. out of control as they are shut down by the pulse. Then Thessia. Resistance forces watch as Reapers start to topple over. It happens all across the galaxy. Reapers fall silent, the galaxy is saved.
On the Citadel, the Creators, minus Harbinger, watch as Shepard falls to the floor, his body being torn apart. They tell him that the synthetics may rise up again. In fact they probably will. As the Creator's disappear (the Reapers they represent being destroyed), Shepards final words are that whatever lies ahead, they deserve to choose it for themselves.
We then have an epilogue where we see the squadmates enter the Citadel. The LI finds and holds Shepard's dead body in his/her arms. Finally, a montage of the rebuilding of worlds across the galaxy as we hear a voice over from Liara - her description of Shepard recorded earlier in the game. Final shot sees us on Earth, rising from the planet as the sun sets behind it, the trademark horizon line of Mass Effect. Credits.
Obviously, depending on various choices, you could end up with various other endings, such as the Relay destruction, the Reapers winning or the galactic races becoming Reapers. If you get the ultimate "let the galaxy decide it's own fate" ending where Shepard dies...it's possible to have Shepard live but you have to work really damn hard to get it.