Cmdr. Ken Shepard wrote...
Refining characters and not straying too far from established canon. I'm willing to stretch it a bit for personal happiness but don't wanna go overboard.
I'd thinking chapter one will be something along the lines of discovering the body of Shepard, and after-crucible coordination using Hacket's point of view until I can tie in a conscious Shepard. Not sure how I should explain Shep's injuries, or ability to live with blown cybernetics (might leave this as a miracle sorta thing). My main thoughts were building into the new government that must come into play, rebuilding and Shep's role to the council and new promotion (in retirement) to Admiral. I've thought of making him Earth's Councilor or maybe even a Prime Minister type figure, and adding the Quarian's, rebuilt/salvaged Geth (which I'm not technical enough to even imagine if it might be possible). I wanna touch on politics, especially with everything being so new, plus it allows for an analyzation of where we are as a culture of how we view government.
I want the happy story stuff, white picket fence, marriage to LI, kid on the way...perfect life and then problem within the story. Issue is whats left? Reaper creators are semi-Missing in Action...do I have them come looking for their creation? Maybe this creator-Reaper is a God-like reaper?
My concern is doing something that feels connected to the story. I've read some fanfic (haven't read anyone's here yet tho) that is like all filler, and no real story. I don't want that.
Sorry for my ramblings, been up for a few hours in the early am staring at a rough draft and playing ME3 (again)
Hrm, well, it seems you have a decent idea of what you want to do, just with missing details and unmade decisions and whatnot that would give your story wheels.
In terms of a villain after the reapers...I would say that trying to upstage the reapers would be difficult. Recall that the Reapers were the tools of the Starkid AI, and IIRC the reapers were based off of the primary space-faring lifeforms at the time. Don't know what reaper creators other than the Starkid AI that would exist. That, and the AI stated the Reapers don't really serve a worthwhile purpose anymore once Shepard makes it to the top.
I think that, while it's a popular post-ME3 story arc, the most logical course of action for a villain would be galactic politics. The reapers have been destroyed due to everyone banding together, but can that peace hold? Is cerberus still functional? What about other species' spec ops and Cerberus equivalents?
There are a lot of twists that you can do with it. Some stories utilize ME3 plot arcs to expand the post-ME3 political realm. Some have the council collapse under the weight of their previous mistakes, sometimes bringing Shepard in to fix it...sometimes bringing Shepard in as a scapegoat to sentence to death for war crimes in order for them to show some semblance of control over the galaxy. Some have Cerberus return with a vengeance. Some have mysterious organizations emerge with mysterious tech. Some have all the species battling indoctrinated forces on their homeworlds. Some have Shepard and co helping take back Omega, rebuilding Tuchanka, keeping the peace between certain species, bringing up new species under council space, Etc. Etc.
It might seem smaller in scope, but it's quite interesting stuff, and can be made out to be as dangerous. Deception and backstabbing are harder to fight than Reaper forces in some ways because you can't see it coming. It's not something you can fire a gun at.
Of course, if you want to have a god-reaper, I'd say go ahead, but the Reapers WERE crafted as gods by Bioware. Their concepts were heavily influenced by HP Lovecrafts creations, like Cthulhu and so forth. One upping gods is...it would require some amazing level of rationalization to sell me on the idea. That's just me though. *shrug*
There doesn't need to be a single overarching villain, or even a stable enemy. it could very well come in bursts across the story, certain challenges arise. There are a lot of open plot threads after ME3. Writing about Shep and co closing those threads isn't the worst idea, and it would allow you to stick close to the canon.