WARNING: The following article contains spoilers for Godzilla: The Planet Eater, streaming on Netflix now.
Godzilla: The Planet Eater is the final chapter in the new anime trilogy that began with Planet of the Monsters. Following last year's City on the Edge of Battle, this film picks up with Earth's survivors, led by the soldier Haruo, joining with the mystical race known as the Houtua to kill Godzilla.
After Haruo stops the Mechagodzilla City and its sentient nanotechnology from spreading across the globe, he basically destroys their only hope of taking down the King of the Monsters. However, his ally Metphies, a priest of the alien Exif, offers a solution: the cosmic three-headed dragon King Ghidorah. That leads to a monstrous, yet cerebral, finale that reshapes the future of Earth.
KING GHIDORAH ARRIVES
We find out that Metphies is actually the avatar for Ghidorah, who uses Haruo's soldiers as sacrifices in a ritual that opens portals for the dragon to arrive from another dimension. The "Golden King" goes on to incapacitate Godzilla, but to make his form physical on this plane, Metphies needs a worthy sacrifice.
That's why he's been goading Haruo to become a believer and a priest. Once Haruo accepts the dragon as his new god and lays down his life, that will allow Ghidorah to appear in the flesh, kill Godzilla, and raze and devour the Earth. When Haruo confronts Metphies, the holy man locks him in a trance using his magical eye, corrupts the soldier so his religious mission can be fulfilled.
MOTHRA'S LIGHT SAVES THE DAY
However, one of the Mothra twins, a Houtua woman named Maina, realizes Haruo is being used as a conduit. Driven by her love for him, she goes to the Mothra egg her people worship, and get it to shine its magical light into Haruo's mind. It purifies the soldier, and stops him from giving in to the chaos and destruction Ghidorah would bring, thus allowing Haruo to understand Metphies was actually playing mankind all along.
He damages Metphies' eye and, after their standoff, the priest is left near death. More importantly, his connection to the dragon finally has been broken. As a result, Metphies becomes the sacrifice, and Ghidorah's energy becomes corporeal, allowing Godzilla to physically make contact at long last. However, Ghidorah underestimates Godzilla, who begins squashing his foe, neck by neck. Godzilla uses his atomic blast to finish killing Ghidorah and to destroy the portals the dragon created, thus ensuring the real Ghidorah never enters this dimension.
MANKIND SURVIVES... FOR NOW
With Metphies dead and Ghidorah banished, Haruo and his remaining warriors integrate with the Houtua, with the soldier going on to marry Maina. However, when mankind reactivates the nanotech that bonded with Yuko (one of Haruo's comatose soldiers from City on the Edge of Battle), Haruo decides to make another sacrifice, as this ambition is what placed mankind in danger in the first place.
He remembers Metphies' words that such advancement will bring with it hubris, and humanity will once more become a species of war. Haruo finally understands this path will result in another battle with Godzilla, thus creating an opening for Ghidorah to return once humans get desperate enough to turn to the Exif again. And so, he leaves his wife and unborn child behind, taking Yuko's body in the last remaining jet and attacks Godzilla. It's a kamikaze mission that results in them being incinerated by the beast's atomic breath.
As much as he is a destroyer, Godzilla actually saves humanity this way, and Haruo dies an honorable death. This sacrifice ensures mankind will remain in a primitive state, surviving in a prehistoric future with no technology and with Godzilla as king.