i don’t think any games of the sort you need are on PC (least of all less violent ones), i would say Mario 64/Sunshine, but obviously not pc . . . so i’d suggest tomb raider or Final Fantasy VII, but the problem is these are much more linear than most people seem to realise (they are on PC and PSX btw)
personally i know of people that cant stand the FFVII plot. they are not my friends as i cant respect that opinion. it is genius, but playing to get to the interesting bits can take 20+ hours of faultless play as its so big.
my only other suggestion is Metal Gear Solid, again PSX and PC (i think . . . ) but again i have yet to see a truly non linear plot driven game on any format.
hope something might help