That reminds drag of Halo, though significantly more silly.

In Halo, the Covenant are on an interstellar crusade for holy artifacts left behind by the Forerunners. When they discovered the planet Harvest, inhabited by humans, they saw tons of artifacts on their scanners. So naturally, they landed on the planet and started blasting the humans to steal the artifacts. But the more humans they killed, the more artifacts disappeared from their monitors. The humans must be destroying the artifacts out of petty spite! What heresy!

The Prophet of Truth is curious about what kind of artifacts the humans have, so he goes to talk to an ancient Forerunner AI they have in storage, Mendicant Bias. Truth shows Bias the symbol that they keep seeing on human worlds. Bias says "You fool, you've got it upside down. Turn it around, see? It says Reclaimer. It means a person the Forerunners have chosen to inherit their empire. You've just been killing these humans? No wonder the reclaimers keep disappearing, you're the one who's doing it!"

So Truth realises that he's been ordering his troops to kill what should rightfully be considered demigods by his religion, and who he should be worshipping. And he realises that if he reveals this information to the people, he and the other Prophets will lose all their political power since there are Actual Fucking Gods walking around. So naturally, Truth declares a Holy Genocide against humanity so that nobody will ever figure out that he's guilty of Deicide and that their entire religious political structure is a lie.