: This seems to meet the criteria of your description, and I've never really
: seen anything outside of content on the story page that's as in depth
: about marathon as you're saying:
: https://marathon.bungie.org/story/Philtron_Inifnity_analysis.html
That wasn't "late aughts". (And, bluntly, I don't recommend that one as it discards the dream levels--along with at least one normal-level terminal that leads to them--and makes a number of unsupported assumptions.)
The closest I can think of the kind of "essay" ArgoMarrus was asking about might be a Tour of Duty. And while this still isn't late aughts, my friend Hokuto did a play-along of the entire Marathon Trilogy on Dreamwidth back in 2015.