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.

Humanity finally rids themselves of Godzilla, imprisoning him in an icy tomb in the South Pole. All is peaceful until various monsters emerge to lay waste to Earth's cities. Overwhelmed, humanity is seemingly saved by a race of benevolent aliens known as Xiliens. But not all is what it seems with these bizarre visitors. If humanity wishes to survive, they must reluctantly resurrect their most hated enemy, Godzilla.

The U.N.G.C.C. (United Nations Godzilla Countermeasure Center) recovers the remains of Mecha-King Ghidorah and construct Mechagodzilla as a countermeasure against Godzilla. Meanwhile, a giant egg is discovered along with a new monster called Rodan. The egg is soon found to be none other than an infant Godzillasaurus.

A demonic reincarnation of a Japanese general from the 10th century appears in the early 20th century Tokyo with a mission to destroy the blooming city.

Kyogokudo is a used book seller who doubles as an onmyouji, or Heian style occultist. His friend Sekiguchi brings him the story of a woman who has been pregnant for twenty months. Sekiguchi investigates further with the help of his friend Enokizu, a detective with the unusual ability to see people's memories. They are hired by the impossibly pregnant woman's sister to find the woman's missing husband and lay this whole matter to rest. In the end, they need the help of Kyogokudo to exorcise the family curse.

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.

A mysterious extraterrestrial being resembling Godzilla rapidly approaches Earth. The monster, dubbed SpaceGodzilla, lands to challenge the King of the Monsters.

An independent group of researchers called the Godzilla Prediction Network (GPN) actively track Godzilla as he makes landfall in Nemuro. Matters are further complicated when a giant meteor is discovered in the Ibaragi Prefecture. The mysterious rock begins to levitate as it's true intentions for the world and Godzilla are revealed.

An Okinawan prophecy that foretells the destruction of the Earth is seeming fulfilled when Godzilla emerges to return to his destructive roots. But not all is what it seems after Godzilla breaks his ally Anguirus's jaw. Matters are further complicated when a second Godzilla emerges, revealing the doppelgänger as a mechanical weapon.

A group of ruthless gangsters, an unknown woman and an escaped convict have met, in The Forest of Resurrection, the 444th portal to the other side. Their troubles start when those once killed and buried in the forest come back from the dead.