Been having a big think about this and I’ll bring some not yet mentioned games into the mix.
JAK 2 - This has a weirdly good story, considering how much of a “games need to be grim” it outwardly has. It’s a huge departure from the first game in the series, but is still connected in smart important ways. It’s kind of like “kiddies first cyber punk thriller.” Feels a lot like a well made early 2000s cartoon with lots characters and is full of charisma.
Knights of the Old Republic 2 - The first KOTOR is a traditional star wars story in a new setting. KOTOR 2 does something which I think is far more brave and for me pretty thrilling. It attempts to create a different and daring kind of star wars story. It even manages to begin to ask question of “What even is the force anyway?” which is neat! It’s my favourite Star Wars thing ever. Shame the game it self is unfinished.
Bioshock 2 - Another sequel which I kind of like more than critically acclaimed original. Bioshock 2 is the surprisingly touching story of a child being in the middle of a dispute between her two parents. Plus one of your weapons is an industrial drill which feels pretty great.
Dragon Age Origins - The best humdrum fantasy story ever made in a game. The story isn’t massively creative or original, but it still hits all the right beats. Sometimes that’s all you need you know.
Something super inspired that DAO does do is the effects a characters origin stories have on the overall story. A characters origins often effects the context of how the main story plays out. I don’t think I’ve ever played a game that does this one thing as well as Dragon Age Origins.
LOOM - Oh, it’s just wonderful. Even comes with an audio book.
Dark Souls (and souls games/bloodborne) - I love Souls stories, but I would be lying if I said I understood anything that was going on while playing the games themselves for the first time. I enjoy the stories in retrospect.
Dead Space - Okay, Dead Space has a bad story, full of stupid conspiracy junk and dozens of logical inconsistency’s and what not, BUT the main core of Dead Space’s story, a man wandering onto a spaceship and then immediately realising the situation is out of control and everything confusing, stressful and weird, that is the compelling nugget for the story.