Perhaps quests that are tied to certain spawning structures, such as say Avian tombs or Apex labs, an NPC will spawn somewhere in the world with the task for you to clear out the dungeon and/or retrieve something from inside
Just wanted to signal boost this idea. I think it's really smart, sort of an 'oh, durr' level of introduction.. I mean, who wouldn't love to see a lone robot, standing outside his evidently over-taken lab? The goal? Clear out the two crazed robos inside! There's a sewer? A lone Apex tells you that his favorite sword was lost inside the sewer. Grab the quest item from the chest and return it for a reward! (Or keep the sword and kill the quest-giver!) This could tie into crashed wreckage, where the player must 'assist' a survivor by bringing them food or medical kits.
If we can even take it a step further, it would be great. Something like finding quest start items at the end of dungeons, or even the dungeon linking to a chain itself. For example, you raid a tomb and don't find the quest item inside. You refer back to the quest giver, and they tell you that they must have brought it back to their home base at (x,x). Or even saying something along the lines of "They're in cahoots with this pirate ship that wanders around the system. Please, find it for me!' and then you must search every planet/moon in the system, but for a major reward. But rather than resources, which are easy to find, you should get rewarded possibly with rare or legendary weapons, or upgrade tokens as I mention in this thread.
Well if at the start of every dungeon there was a chest with a book and that book contained the quest then i would have a reason to go in other than getting useless weapons and minimal pixels