The Millennium series is treated similarly to an anthology series where each film is a standalone story, with the 1954 film serving as the only previous point of reference.
北海道・根室にゴジラが出現した。現場にいたゴジラ予知ネット（ＧＰＮ）を主催する篠田と小学生の娘・イオ、そして取材で同行していた雑誌『オーパーツ』の記者・由紀は、間近に見たゴジラに人間の作り出すエネルギーに対する憎悪を感じるが、果たしてゴジラは根室近郊に建つ巨大発電所を破壊する。同じ頃、茨木県沖の日本海溝では巨大な岩塊が発見されていた。危機管理情報局（ＣＣＩ）の内閣官房副長官である片桐は、科学者・宮坂を使って調査に乗り出すが、それは6千万年から7千万年前に地球に飛来したＵＦＯだったことが判明する。ところがその時、東海村の原発を狙って再びゴジラが現れる。しかも、ゴジラに向かってＵＦＯが飛行を開始。対峙したゴジラとＵＦＯは一戦交えるが、互いの力は五分と五分。ゴジラは海中に飛ばされ、ＵＦＯも墜落してしまう。しかし、先に蘇ったのはＵＦＯだった。その後、新宿に飛んだＵＦＯは由紀の会社のあるシティ・タワーの屋上に到着する。地球を侵略すべくコンピューター・ネットに侵入し、地球改造計画を開始する。だが、そこへ復讐に燃えるゴジラが登場した。壮絶なバトルが再び展開され、ゴジラはＵＦＯを叩き壊すが、その残骸からゴジラの細胞組織であるオルガナイザーＧ1を吸収した怪獣オルガが出現する。またもやオルガと激しく戦い、みごとオルガを倒すゴジラ。しかし、ゴジラの人間に対する攻撃は終わっていなかった。高層ビルが林立する新宿で暴れ回るゴジラを止められるものは、もはや誰もいない。
The prologue of the film acknowledges the events of the Godzilla (1954 film) (using the 1954 Godzilla monster rather than a successor Godzilla), while inventing its own timeline, explaining that the Oxygen Destroyer was never used here and that the capital of Japan was moved from Tokyo to Osaka. The film takes place in an alternate universe with advanced technology, explaining that in 1966, Godzilla attacks the first Japanese nuclear plant in Tokai, Ibaraki, Ibaraki Prefecture. After this, the G-Graspers, a section of Japanese Self Defence Force, was dedicated to fight Godzilla. In 1996, clean plasma energy replaced nuclear energy, but this did not deter Godzilla from attacking. Plasma energy is also banned, due to the fact that Godzilla attacked the original plasma energy Fusion power.
During a meeting of the Japan Self-Defense Forces (JSDF) for the potential return of Godzilla, Admiral Taizo Tachibana briefs cadets about Godzilla's first attack. A nuclear submarine is reported missing, which is later found to have been destroyed by Godzilla. Tachibana's daughter, Yuri Tachibana, films a docudrama with her crew for BS Digital Q at Mt. Myoko, where a mysterious earthquake randomly ensues. The odd earthquake returns later that night burying a biker gang and leaving one surviving trucker who witnesses the monster, Baragon.
After the appearance of a new Gojira (Godzilla), the Japanese government builds a robotic Godzilla from the bones of the original monster that attacked Tokyo in 1954 to stop the beast.
In 2004, Mechagodzilla is undergoing repair modifications after its battle with Godzilla one year earlier. Prime Minister Hayato Igarashi accepts Lead Scientist Yoshito Chujo's choice to replace the Absolute Zero Cannon with a powerful Tri-Maser.
Years after an initial attack of Tokyo in 1954, Godzilla is entrapped under ice in Antarctica after a battle with the original Atragon. In later years, environmental disasters cause the appearance of giant monsters and superhumans, dubbed "mutants", who are then recruited into the Earth Defense Force (EDF) to battle the monsters. An upgraded Gotengo, commanded by Captain Douglas Gordon, battles and destroys Manda (kaiju), but the ship is wrecked in the process and its captain is suspended from the EDF.