Woowwww this was neat. An adventure, like you say! Love the very distinct (and massive) areas. The environment lighting is quite a bit darker than "Quake standard", but cranking my gamma fixed that.
I always like ambitious use of underwater environments in Quake. Although it took me a second to figure out the ladders were "extras_r5 style" in how they worked! And generally items/vehicles made out of brushes (submarines etc.) is a thumbs up.
I did get stuck on finding the "air shaft" for a bit, but solved that through some spatial reasoning which felt good. The only puzzle-ish thing I really failed at, I think, was trying to get to the red armor just inside the main temple entrance. That one is a real mystery! (Although BTW it's kind of bogus that an invisible wall there blocks grenade-jumping.)
The final room is excellent, both the construction and also how you staged the waves. One bit of the fight was a little anti-climactic, where one of the last shamblers I had to kill was just way off on a staircase chilling by himself until I hunted him down... but that's the Quake AI for ya I guess.
This map won't be to everyone's taste but IMO you nailed what you were going for.