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.

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

JSDF pilot Akane has a fateful encounter when a new Godzilla emerges in Tateyama. As a countermeasure, a cyborg named Kiryu is constructed from the remains of the original. The machine is discovered to harbor the restless soul of the original monster as Akane must learn to find value in her own life as well.

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.

During WWII, Germans obtain the immortal heart of Frankenstein's monster and transport it to Japan to prevent it being seized by the Allies. Kept in a Hiroshima laboratory, it is seeming lost when the United States destroys the city with the atomic bomb. Years later a wild boy is discovered wandering the streets of the city alone, born of the immortal heart.

Mining engineer Shigeru investigates the disappearance and death of his fellow coworkers when prehistoric nymphs are discovered emerging from the mines. After an attack on the local village, Shigeru heads deeper into the mines only to make a more horrifying discovery in the form a prehistoric flying creature. Soon a second monster appears as the two converge in Fukuoka.

A horrifying hybrid of genetic science and nature has taken over the Louisiana bayou, leaving terror in its wake! In the heat of the summer, what began as an day of boating and bikinis changes drastically when a school of genetically enhanced snakehead fish finds their way into Black Briar Swamp.

Mothra's dark counterpart, Battra, emerges to eliminate humanity on behalf of the Earth. Two tiny fairies called the Cosmos offer their help by calling Mothra to battle the creature. Unfortunately a meteorite has awoken a hibernating Godzilla as a three way battle for the Earth begins.

An ever evolving alien life-form arrives on a comet from the Dark Gaseous Nebula and proceeds to consume pollution. Spewing mists of sulfuric acid and corrosive sludge, neither humanity nor Godzilla may be able to defeat this toxic menace.

In order to protect the reputation of the American space program, a team of NASA administrators turn the first Mars mission into a phony Mars landing. Under threat of harm to their families the astronauts play their part in the deception on a staged set in a deserted military base. But once the real ship returns to Earth and burns up on re-entry, the astronauts become liabilities. Now, with the help of a crusading reporter, they must battle a sinister conspiracy that will stop at nothing to keep the truth hidden.

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.

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.

A burning Godzilla, on the verge of meltdown, emerges to lay siege to Hong Kong. At the same time horrifying new organisms are discovered in Japan. These crustacean-like beings are seemingly born of the Oxygen Destroyer, the weapon that killed the original Godzilla.

In 1889, seventeen men die under mysterious circumstances, and spooked by recent events, the miners who populate the town leave in droves until there's nothing left but a shell of a community.

The advertising director of Pacific Pharmaceuticals, frustrated with the low ratings of their sponsored TV program, seeks a more sensationalist approach. He orders his staff to Faro Island to capture King Kong for exploitation. As Godzilla re-emerges, a media frenzy generates with Pacific looking to capitalize off of the ultimate battle.

After the previous Godzilla attack, a miniature arms race ensues to collect his cells. Concerned over Godzilla's possible return, the Japanese government uses the cells to create a new bio-weapon, ANEB (Anti-Nuclear Energy Bacteria). They seeks the aid of geneticist Genshiro Shiragami, who's experiments result in a new mutation.

A desperate group of refugees attempts to recolonize Earth 20,000 years after Godzilla took over. But one young man wants revenge above all else.

In Beijing, a young martial artist's skill places him in position to experience opportunities and sacrifices.

Japan is thrown into a panic after several ships are sunk near Odo Island. An expedition to the island led by Dr. Kyohei Yamane soon discover something far more devastating than imagined in the form of a 50 meter tall monster whom the natives call Gojira. Now the monster begins a rampage that threatens to destroy not only Japan, but the rest of the world as well.

Fourteen years after Third Impact, Shinji Ikari awakens to a world he does not remember. He hasn't aged. Much of Earth is laid in ruins, NERV has been dismantled, and people who he once protected have turned against him. Befriending the enigmatic Kaworu Nagisa, Shinji continues the fight against the angels and realizes the fighting is far from over, even when it could be against his former allies. The characters' struggles continue amidst the battles against the angels and each other, spiraling down to what could inevitably be the end of the world.