Μια κρυφή ζωολογική ομάδα, παρακολουθεί από κοντά την εξέλιξη και τη δράση μυθικών πλασμάτων που ζουν στο βυθό της θάλασσας. Ανάμεσα σε αυτά, είναι ο Godzilla που θα βρεθεί για άλλη μια φορά και πάλι υπέρ της ανθρωπότητας, καθώς θα αντιμετωπίσει τέρατα όπως τους Mothra, Rodan αλλά και την απόλυτη νέμεση του, τον τρικέφαλο βασιλιά Ghidorah. Οι μάχες του θα παίξουν θεμελιώδη ρόλο στην ισορροπία του πλανήτη και το μέλλον της ανθρώπινης ύπαρξης.

Με τη γήινη συμμαχία να έχει αποδυναμωθεί, ο Χάρουο σκέφτεται να συμμαχήσει με τους Έξιφ, η αίρεση των οποίων καλεί ένα τέρας που μπορεί να καταστρέψει τον κόσμο.

Godzilla has become a distant memory for Japan when the destruction of a US submarine raises alarms for Admiral Tachibana. His estranged daughter Yuri investigates the legend of the guardian monsters, who must rise to protect Japan against the vengeful spirits within Godzilla that seek to destroy both the nation and its people for the suffering they inflicted in the Pacific conflict.

The Futurians, time-travelers from the 23rd century, arrive in Japan to warn them of the nation's destruction under Godzilla. They offer to help erase Godzilla from history by preventing his creation. With Godzilla seemingly gone, a new monster emerges as the Futurians' true intentions are revealed.

Astronauts Glenn and Fuji investigate Planet X and encounter mysterious aliens known as the Xiliens, who ask Earth's people to help save their world from "Monster Zero". In exchange for borrowing Godzilla and Rodan, the Xiliens offer a cure for cancer. As Glenn investigates, he develops a romance with Miss Namikawa and uncovers the Xilien's true intentions.

At the turn of the century, all of the Earth's monsters have been rounded up and kept safely on Monsterland. Chaos erupts when a race of she-aliens known as the Kilaaks unleash the monsters across the world.

Manga artist Gengo Odaka lands a job with the World Children's Land amusement park only to become suspicious of the organization when a garbled message is discovered on tapes. As Gengo and his team investigate, Godzilla and Anguirus quickly decipher the message and begin their own plan of action.