I have a carbon hardtail which I used to ride the Great Divide MTB route last summer. About halfway through I had a similar issue which I couldn't seem to resolve; a creak everytime I put power through the pedal stroke. I took apart and cleaned the cranks, pedals, axle, checked BB bearings for play, etc... No change.
Finally, I took my bike in to a local bike shop when we got to the next town and the owner there straight away asked if I'd checked the rear axle. I hadn't as it didn't seem a likely suspect... It turns out, with the large amount of dust and occasional mud the bike had been subjected to and with no opportunity to give it a good thorough clean, some dirt had accumulated between the rear axle quick release clamp and the frame. When I put power through the pedals, the frame was flexing quite significantly ( exacerbated in part because of all the bikepacking gear strapped to it) and causing the axle to creak as it shifted on each stroke. I gave it a good clean, added a drop of lube, tightened it up and... hey presto, problem solved.
Not guaranteed to be this but it's an easy thing to check (especially compared to pulling out your BB) so worth having a look.