I was pretty sure the mage boss was elaborately failing to mention that the Enormous Mentor Bird was actually the Owl King, who wanted the battery for nefarious purposes. Which wouldn't make sense actually; the Owls are in charge of the whole facility until you kill them all. Maybe something else similarly nefarious.
This was a decent game. I think a 'skip cutscene' option, and maybe a run button, would have been big helps - the backtracking felt unreasonably padded, and the second bossfight was extremely frustrating because the death penalty was unusually large.