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Sometimes final boss is unresponsive until some unclear event triggers it. In this dormant state it regenerates any destroyed zooids instantly and indefinitely and doesn't have protective red shell on its primary zooid. This may happen more often when I sneak around and kill a few mini-bosses first. Perhaps it's something with boss ai, as it's quite complicated as I can see.

Thanks for the report!

It may be caused Frakir being unable to fully grow and still be in the "preparing for battle" state. I think I see a missing spike. Noted!