WARNING: The following article contains spoilers for Godzilla: The Planet Eater, streaming on Netflix now.
Toho's Godzilla: The Planet Eater closes out the new anime trilogy in which humanity is driven from Earth by the King of the Monsters, only to return decades later to try to take back their world. But as the story unfolded from 2017's Planet of the Monsters to last year's City on the Edge of Battle, many viewers wondered whether mankind or Godzilla was the villain.
In this final chapter, however, we learn it's neither.
When Haruo, the leader of Earth's resistance, is left with one last option, to summon King Ghidorah, the true villain of the trilogy is revealed to be the species that goaded our hero to this point, the alien species the Exif. Specifically, it's Metphies, the high priest who offered Haruo counsel in the first two movies, and served as his spiritual guide and moral compass.
In the first two chapters, the Exif were an alien-humanoid race that, along with the Bilusaludo, befriended humanity after it abandoned Earth. The religious Exif offered hope and inspiration, leading to Metphies becoming Haruo's best friend. But as Metphies tries to convince him here to become an avatar and eventual sacrifice for Ghidorah, it becomes clear the Exif are actually a cult that travels the universe, scouting civilizations that reach their peak. They then manipulate them into then offering their lives to the three-headed dragon so that it may arrive in this dimension and bring order to their planet. However, the price of order is annihilation.
That's what occurred on the Exif's home world, and now the aliens are offering other planets as tribute to Ghidorah. All they need is to complete a ritual to summon Ghidorah from his own dimension. To that end, they identify a species at its breaking point, in hopes of converting it into a religious disciple. Once a species willingly becomes a sacrifice, Ghidorah's essence enters the dimension, and he devours its planet. Metphies and his minions prey on humanity's fragile state, and go so far as to kidnap the Mothra twin Miana and attempt to use her as a sacrifice too.
Viewing the dragon as a purifier, the Exif seed priests like Metphies throughout the cosmos. It's his role to convince a species that the "golden king" is the solution to its problems. Having created Godzilla, thus driving themselves to despair and desperation, humans are a relatively easy mark.
After Haruo survived the nanotech virus from Mechagodzilla city in City on the Edge of Battle, Metphies makes him a messiah. He then converts Haruo's followers into his own cult members, and then sacrifices them to Ghidorah. The Exif aren't completely selfish, however, because they believe Ghidorah is a god and this is a blessed apocalypse. It's only when Haruo's mind is purged by the light of Mothra that he realizes it was Metphies who, in Planet of the Monsters, destroyed a ship transporting old people (including Haruo's grandfather), so that their space station would have fewer mouths to feed.
But as we find out, it was more than just a survival decision: Metphies was playing Haruo and driving him to the brink of a mental breakdown, turning him on the station itself. That made Haruo desperate enough that, in The Planet Eater, he'd want to offer himself to Ghidorah and bring the monster to Earth. He thought he was summoning a savior, but all he was really doing was welcoming a destroyer, thus dooming his home world. Godzilla may have been evil, but he was the lesser of two, as the Exif was a quiet, cerebral Judas devoted to destroy humanity from within.