In my own personal opinions, Synthesis was actually a pretty good ending. The idea that it "mind rapes" the Galaxy isn't what I imagine happens. I think what happens is that organics receive physical augmentations, like stronger muscles or faster reflexes, while synthetics gain a better understanding of sentience-emotion, creativity, sensation etc. NOT turning everybody into husks. Other than that, we get friendly Reapers, a long-term solution to the "organic/synthetic war" problem, the geth and EDI doesn't die, and so on.

So of course, the only major problem is the death of Shepard. I can accept Shepard's death in-canon, but that doesn't stop me from making my own :)

"The paths are open. But you have to choose."

The Catalyst looks on at Commander Shepard, the human woman standing before the choices laid before her. She was on the verge of death, her body scarred and her armor scorched. Trying to push aside the pain, she weighed the options she had.

The Catalyst, thinking to itself, had to give her credit. No organic had ever reached this far, no cycle had ever put up such a fight. This "Shepard" achieved some impressive feats over the last few months. She had changed the variables, and the Catalyst had just given her the chance to shape the future of the Galaxy. "Worry", something the Catalyst had not felt in a very long time, sank in. In two of the choices, the Catalyst itself and the Reapers was either destroyed or absorbed into Shepard's consciousness, and both left a lot of room for error. The Catalyst's destruction would leave the question of organic-synthetic peace unaswered, and nothing suggested Shepard could handle assuming control of the Reapers. But, Shepard had proven that the Catalyst's methods would no longer work, so the final choice was hers.

Not saying a word, Shepard took a step forward, then another, then another, slowly making her way to her choice.

The Catalyst pondered, it was millions of years old, and now it was going to be irreversibly changed in a few seconds. It stayed where it was, watching Shepard take what had to be the last few steps of her life. The Catalyst would never have said it, but it felt "spite" towards the human. Ever since she foiled Sovereign three years ago, Shepard was a constant thorn in the side of the Catalyst. Destroying her had been a primary goal since the Reapers arrival in the Galaxy this Cycle. Whatever she chose, it had to make sure she died in the process. It was a feeling the Catalyst couldn't describe, it could only act on it.

Shepard came to the intersection, and moved straight ahead, towards the beam.

To say the Catalyst was expecting her to make that choice would be a lie. It was the one choice that Shepard, to her knowlege, had no chance of survival. That was a lie of omission on the part of the Catalyst. Synthesis didn't require the individual to be destroyed, their energy acted as an amplifier to the Crucible, a "Catalyst", fittingly-it enhanced the reaction, but was not itself consumed. The "spite" compelled the Catalyst to kill Shepard in the blast, and it still planned to do so.

Then, it realized something.

Shepard and the Catalyst had similar goals: Establish connections between different forms of life, to avoid conflicts of total destruction. That was why the Reapers were created, the harvest preserved the advanced civilizations in Reaper form, avoiding the inevitable war between organics and synthetics and allowing the younger species their time to florish. Shepard, however, succeeded in the methods that the Catalyst tried before the Reapers: The krogan and turians, sworn enemies, now work together. The geth and the quarians, what was to be yet another case of the Catalyst being proved right, now work together. And Shepard had been the reason it all happened. This single human had solved problems the rest of the Galaxy had failed to solve for centuries in months, and assembled one of the largest fleets the Reapers had ever had to fight. Even when all life in the Galaxy undergoes Synthesis, they will not be perfect, peace will not be permanent. Individuals like Shepard will be needed in the aftermath, if the Galaxy is to not fall back into war.

Shepard is now running towards the beam, accepting her fate.

To it's own surprise, the Catalyst makes a decision. It holds back in disintegrating the Commander, allowing the Crucible to analyze her energy, adding it to itself. The Catalyst instructs the beam to transport Shepard back down to Earth. There's something else the Catalyst hasn't felt in a long time. "Mercy"

'No rest yet, Shepard. You still have a lot of work to do.'

The Crucible fires.

I'll be writing chapters on where the many characters end up. Be sure to leave suggestions on who you want to see "epilogued"!