Undertale, since the clever writing and variety don't really kick in until after the Ruins, and the creeping darkness doesn't set in until much later.

NieR has a great opening scene, but it doesn't start to truly shine until Kaine comes in and the dysfunctional duo turns into a dysfunctional group. And then, of course, the rough halfway point starts to introduce what makes the game truly special.

SOMA is pretty standard sci-fi horror until you reach Site Theta and get your brain twisted up in a knot.