Speculation time:
The middle school boy is their half-brother, who for some reason hates Ai. Possibly the spirit girl was his twin sister who died and he blames Ai for that. Furthermore, it's also possible that the boy himself is also the reincarnation of someone else, explaining how he could orchestrate such a plan while being so young and adding to the narrative symmetry he'd have with Aqua.
Now, it's entirely possible, and likely, that I got it all wrong, but it's the best theory I could come up with, considering the information we have up to this point.