Story Spoiler:
I also didn't how Callie was brainwashed. The story would actually be a little interesting if she joined the Octarians by choice, but instead it's actually laughable as the brainwashing served literally no purpose. I guess it's my fault for expecting something out of the story in a Nintendo game.
Oh and I got all the scrolls (which gives you nothing btw) but no info on why an Octarian is allowed in Inkopolis, the thing I was most interested in.