Assuming Ami was being honest with us, I think I can understand the way she's looking at the world, maybe.
Her story, if I had to guess, is one of her seeking meaning, finding none, and having to create it for herself.
She commented early on about how everything was so inefficient. A thousand years of history, of war and death and horror, and we still haven't reached a conclusion. A girl as clever as Ami Mori, with a bloodline of logistics and efficiency, kept searching for the perspective that makes everything click. The goals that actually match what's happening, the ultimate truth of the world.
And she found nothing.
So, if it's now clear that no one's really truly pursuing a meaningful goal, what ideological banner does a girl like Ami rally behind? Can she truly and fully support Mist winning its wars if Mist doesn't fully support that? Instead, Ami eschewed external sources of inspiration and looked inwards. From first principles (or something like it), Ami arrived at what is (to her) the only reasonable goals and ideals. The kind of ideals you get when you take things to their logical conclusion and don't mind where you ended up.
And, with that, Ami pushed herself further while also separating a degree from the people around her. Can she honestly look up to Ryugamine like she used to, now that she's the master of her own ideology? Can she honestly act in service of the Mori's goals if she no longer subscribes to how Mori see the world? And all the same it makes her freer, she's the only one who understands herself so she's not beholden to the opinions of others save how they impact her goals. And as some connections wane new opportunities rise up in turn, such as a talented Genin with ambitions as great and fierce as her own.
Of course, Ami could have lied about many things in our date, and the assumptions I made beyond that may be wrong, but this feels like the kind of story that matches her, the general shape of it even if I turn out to be wildly wrong on the details. What do you guys think?