The film features the fictional monster characters Godzilla and King Ghidorah, and stars Kōsuke Toyohara, Anna Nakagawa, Megumi Odaka, Katsuhiko Sasaki, Akiji Kobayashi, Yoshio Tsuchiya, and Robert Scott Field.

The plot revolves around time-travelers from the future who convince Japan to travel back in time to prevent Godzilla's mutation, only to reveal their true motives by unleashing King Ghidorah onto the nation.

Because the previous installment was a box office disappointment, due to a lack of child viewership and alleged competition with the Back to the Future franchise, the producers of Godzilla vs. King Ghidorah were compelled to create a film with more fantasy elements, along with time travel.

In February 1944, while threatened by American forces, the Japanese soldiers were saved by a mysterious dinosaur, Godzillasaurus, which Terasawa theorizes was subsequently mutated into Godzilla in 1954 after a hydrogen bomb test on the island.

When the JSDF investigates, it is revealed that the UFO is in fact a time machine and they are greeted by Wilson, Grenchiko, Emmy Kano, and the android M-11.

The Futurians, Terasawa, Miki Saegusa, and Professor Mazaki, board MOTHER's time machine, KIDS, and travel back to 1944 to Lagos Island.

Before returning to 1992, the Futurians secretly leave three genetic-engineered monsters called Dorats on Lagos Island, which are exposed to radiation from the hydrogen bomb test in 1954 and merge to become King Ghidorah.

Feeling sympathy for the Japanese people, Emmy reveals to Terasawa the truth behind the Futurians' mission: in the 23rd century, Japan is an economic superpower that has surpassed the United States, Russia, and China, and even bought out the entirety of South America and Africa.

[c] En route to the Bering Strait, Shindo's submarine is destroyed by Godzilla, who absorbs its radiation, recovers from the ANEB and becomes larger.

The film was ultimately scrapped by Toho, under the assumption that, unlike Godzilla, Mothra would have been a difficult character to market overseas.

The planning stages for a sequel to Godzilla vs. Biollante were initially hampered by Tanaka's deteriorating health, thus prompting the takeover of Shōgo Tomiyama as producer.

Ōmori himself blamed the lackluster performance of Godzilla vs. Biollante on competition with Back to the Future Part II, and thus concluded that audiences wanted plots involving time travel.

[3] His approach to the film also differed from Godzilla vs. Biollante in his greater emphasis on developing the personalities of the monsters rather than the human characters.

"[11] Film historian and critic David Kalat wrote "Despite its shortcomings, illogic, and overpopulated cast, Godzilla vs. King Ghidorah is crammed full of ideas, richly visualized innovations, a genuine spirit of fun, and some of the most complex emotional manipulation ever to grace the series.

The film was considered controversial at the time of its release, being contemporary to a period of economic tension between America and Japan, but mainly due to its fictional World War II depictions.

Gerald Glaubitz of the Pearl Harbor Survivors Association appeared alongside director Kazuki Ōmori on Entertainment Tonight and condemned the film as being in "very poor taste" and detrimental to American-Japanese relations.

[14] Conversely, Godzilla historian Steve Ryfle said American media reports of supposed anti-Americanism "weren't really thought-provoking or insightful.