the owl and the olive tree

I may have watched FLCL too many times, to figure this out, but I'd argue there's a narrative buried beneath the insanity and all the unreliable narrators. Haruko comes to Earth to bash Naoto's head in with a guitar to make him into a kind of gateway. She wants the power of the Pirate King, which seems to be pretty impressive judging from the last episode. Medical Meccanica imprisoned him, or something, so that's why she needs Naoto's head. There's a lot of other stuff that happens, which all makes a bizarre kind of sense in the right light—I can attempt to explain if you're curious.