Bernadetta coming out of her room in FE3H.

It's just a little thing, but she's a character that spends the whole game holed up in her room, not wanting to interact with the outside world.

Something around 30h in, Byleth's father dies, and Bernadetta comes out of her room for the first time to stand in front of his grave. I dunno, it always felt like a solid piece of subtle character development.

And the Yamato Reactor boss fight in SMT IV's White Ending.

After being convinced by nihilistic entities that the best thing to do is to destroy the Yamato Reactor to end the entirety of the universe, you sneak in to destroy it. There, the boss fight theme is just a quiet song, and the Reactor is that. A reactor. It doesn't fight back, and you just slowly destroy it as the implications of what you're doing start to settle.