These may or may not be of any use. I like to think I do all right, but heck, everyone's method varies when it comes to writing.

Anyway:

1. Pick your stopping point ahead of time. There's no rule that says you have to get through the entire fic, just that the canon has to be definitively broken, usually an event that stands out from the badness level of the rest of the story, but not necessarily. Sometimes the agents have to wait for an opportune moment to strike, savvy?

2. Pick your talking points ahead of time. I like to keep a copy of the badfic in a document on my computer, so that way I can go through and highlight things that I definitely want to cover and also keep track of minis, any other recurring mistakes, particularly hilarious bits, etc. This way, you have kind of a road map to follow when writing. You probably won't cover everything you highlight, though. This is okay. You have to pick and choose to get a balance between emphasizing ongoing problems, avoiding repetition, and not dragging the mission out past being fun, and some things just aren't as important as others (even if they are still bad).

3. Re-read a lot. When I get stuck, I find that it's usually because I took a wrong turn earlier in the story, and I can't move on until I've located it and fixed it. This often means re-writing large chunks of story, but it's worth it.

4. If it's not fun anymore, you're doing it wrong. Go do something else and come back in a fresher mood. This, too, may result in re-writing.

Aster's right, though—we probably all bite off more than we can chew at some point. The first mission I attempted was a co-write with another Boarder at the time, of a really long, canon-wrecking but otherwise well-written Farscape fic. It . . . totally bombed. The actual point of canon rupture was a LONG way in, and we never got past the first chapter. The fic was later deleted. Such is life.

But, it is important that the fic is bad enough to sustain humor, which in retrospect I don't think that one was. I only pick fics with really terrible "so bad it's funny" writing in them now. In addition to keeping with the rule of "the author must show no sign of actually caring about their work," they're simply much better material for humor.

~Neshomeh

I often hit the 'this mission is too enormous' problem, myself. I have two missions in the works at the moment, but one of them (although I have the plot plotted) is just... SO BAD that I am having trouble even writing it without falling into 'this is bad. This is also bad. Here is another bad thing. when did this become a MST?'

The other one is 60+ chapters of badfic. I think I might get through ten, at the most. But it's already 16+pages and the Sue is making me want to eat my hat.

But don't worry. Missions are hard to write: they're a whole new kind of genre and style of story and as such it takes lots of practice to get down.

Something that, due to the high turnover of writers, is not often attained. I don't have it yet. I hope somebody with more missions under their belt gets to this post! >_>;