Here is what appears to be a fairly simple map:

Volume 1
X-Men 2099 1-5
Doom 2099 14
X-Men 2099 6-25

Volume 2
X-Men 2099: Oasis
X-Men 2099 26-35

However, there were a few complications:
1.) The Fall of the Hammer crossover – a five part story in which X-Men 2099 #5 is part 3.

2.) One Nation Under Doom – a line wide “event”. No direct crossover with the other 2099 titles, though.

3.) X-Men 2099 Special 1 – three stories, only one of which is by John Francis Moore (X-Men 2099′s regular writer)

4.) X-Men 2099: Oasis – a bookshelf story that came out the same time as the end of the series, but must take place earlier.

5.) If binding multiple 2099 titles, there is the concern about how to handle the last few months of the regular titles, when the editor was fired and most creators quit.

Solutions:
1.) Since the crossover hits in issue 5, I couldn’t put a volume break before and after it. And it didn’t make sense to bog down the X-Men collection with the entire storyline, especially since they don’t appear at all in parts 1 and 5. Since their appearance in part 2 was only a couple of pages, and mostly recapped in part 3, I left that issue out. Since John Francis Moore wrote both X-Men 2099 and Doom 2099, and the X-Men are featured quite prominantly in the Doom issue, I opted to only include parts 3 and 4 of the crossover. I do plan on having the entire crossover included in my Spider-Man 2099 volume.

2.) X-Men 2099 was mostly separate during ONUD, doing it’s own thing. No reason to muddy up the story, unless you were binding all 2099 titles together in chronological order.

3.) I skipped the special. None of the stories really mattered overall, and I couldn’t figure out where to put it.

4.) Several places online want to put Oasis between #26-27. That’s impossible if you actually read those issues. The best place would be between #25 and 26.

5.) JFM stayed on board X-Men 2099 until the end, and wrapped up the X plots. The rising water/Atlantis war subplots in the other books was mentioned and used as a backdrop in the last two issues, but it would make sense to just keep the X-Men issues together. I’ll explain X-Nation 2099 and 2099: World of Tomorrow in my World of Tomorrow map.