When I boot up Master.esm and activate any location ID, there is extremely dense fog in the render window. When I zoom out, the map becomes incomprehensible.

Another interesting similar case is the aaaMarkers ID. When I load it up, the background is all black, and when I zoom out, every object disappears.

This hasn't happened before. The night/day cycle if I remember correctly also is broken.

Any help is appreciated.

Try deleting your INI files and re-validating them from Steam.

How may I do that, specifically?

Delete SkyrimEditorPrefs.ini and SkyrimEditor.ini in your main skyrim folder. Then go to Tools in Steam, right click Creation Kit, Local Files then Verify Integrity of Game Cache.