Disco Elysium is not exactly devoid of violence and aggression, even if they aren't central mechanics. It's great storytelling but with some mature themes.

Honestly, I thought I'd have an easier time coming up with some other suggestions to throw in but there's usually some ass-kicking in my favorite story driven games.

The Oni platformer games are a little bit fight-centric but not really violent or cruel, and the story is great. Worth looking at.

Another decent one I just thought of is Outer Wilds, it's kind of a myst-like puzzle game where you just explore the world and discover the story as you go.