Set in suburban Las Vegas, Nevada, 10-year-old Lucas Nickle (Zach Tyler Eisen) is being tormented by a bully and his gang. In turn, he attacks an anthill with a squirt gun which terrifies the ants. One ant, an eccentric wizard named Zoc (Nicolas Cage), tries to fight back but is overwhelmed by Lucas. His girlfriend, a nurse ant named Hova (Julia Roberts), attempts to communicate with Lucas, but is saved by Zoc. The leaders of the colony decide to use a potion created by Zoc, to shrink Lucas down to ant size to punish him, for aiding destruction on their hill.
The narrator explains that in 1957, the Soviet Union launched Earth's first satellite Sputnik 1 into orbit. Four years later in 1961, when NASA was putting a monkey named Enos aboard Mercury Atlas 5, astronaut Yuri Gagarin became the first man on Earth to go to space. The Soviets were beating the Americans in every milestone off the planet. Feeling the sense of urgency to overtake the Soviets in the space race, U.S. President John F. Kennedy made a huge statement toward a joint session of Congress on May 25, 1961, stating that before the decade is out, he plans to launch the man to the Moon and return him safely to the Earth.
Several months after the events of The Fly, Veronica Quaife is about to deliver the child she had conceived with scientist Seth Brundle. Anton Bartok, owner of Bartok Industries (the company which financed Brundle's teleportation experiments), oversees the labor. Veronica dies from shock after giving birth to a squirming larval sac, which splits open to reveal a seemingly normal baby boy. The orphaned child, named Martin Brundle, is taken into Bartok's care. Bartok is fully aware of the teleportation accident which genetically merged Seth Brundle with a housefly (a condition that Martin has inherited), and he secretly plans to exploit Martin's unique condition.
In a peaceful little clearing, the remains of a picnic hastily abandoned spark warfare between two tribes of ants. A bold young ladybug finds himself caught in the middle of the battle. He befriends one of the black ants, Mandible, and helps him save the anthill from the assault of the terrible red ant warriors, led by the fearful Butor.
In Manhattan, cockroaches are spreading the deadly "Strickler's disease" that is claiming hundreds of the city's children. Entomologist Susan Tyler (Mira Sorvino) uses genetic engineering to create what her colleague (and husband) Peter Mann (Jeremy Northam) and she call the Judas breed, a large insect (looking like a cross between a termite and a praying mantis) that releases an enzyme that kills off the disease-carrying roaches by speeding up their metabolism. The Judas breed works spectacularly and the crisis is abated. The released population was all-female and designed with a lifespan of only a few months, so that it would only last one generation.
Nobita was reading a picture book. In that he sees Adam and Eve disobeying God and eating the apple in the garden of Eden. Nobita comments that their descendants have to face many difficulties because of Adam and Eve's mistake. Then Doraemon reminds Nobita that he had to do his summer vacation research homework. Then Nobita decides to see his friends research homework. As Dekisugi ranks first in the class, he decides to see his project first. Then Nobita finds that Dekisugi has finished his research on Ninjutsu. Then Nobita goes to see on what is Shisuka researching. Then he finds Shisuka is keeping observatory on The Morning glory plant. Then he goes to see what is Gian doing and he discovers that Gian has done nothing on his project. Then Gian and Nobita go to see what Suneo is doing and they see that Suneo is filling helium in a balloon with a letter containing a telephone card. The person who finds the letter gets the telephone card. He will receive location of where the balloon dropped by telephone, and then he will record it on his map. Then Suneo can record everyday's weather and wind direction. Then Gian threatens Suneo and gets a share of his project. Nobita gets frustrated and blames Adam and Eve.
Godzilla cells brought into space by Biollante and Mothra are exposed to intense radiation from a black hole. The celestial fission creates a highly aggressive extraterrestrial beast closely resembling Godzilla. This "SpaceGodzilla" quickly makes its way to Earth.
In 1993, an asteroid lands in the ocean and awakens Godzilla. The next day, a young man named Takuya Fujita is detained after stealing an ancient artifact. Later, a representative of the Japanese Prime Minister arrives with Takuya's ex-wife, Masako Tezuka, and offers him to explore an island with Masako and Marutomo company secretary, Kenji Ando, and become a free man. Takuya initially turns down the offer, on the basis that he is to be released in another week. But after his ex-wife informs him that his sentence has been reconsidered, he accepts. After the trio arrives at the island, they find a cave behind a waterfall. Inside, they discover ancient paintings, including a picture of two giant insects fighting one another. While studying them, the sun shines through a hole in the wall, and the light points to a small opening in the cave, where they come upon a giant egg. The three hear a pair of voices, which belong to the Cosmos. They keep the earth's natural order in balance, and informs them the egg belongs to Mothra.
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 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.
Nani is a young man who specialises in making fireworks. He lives in a house opposite micro artist Bindu, who runs Project 511, an NGO. Nani has been in love with Bindu for two years and has been constantly showing his love for her. Bindu too loves Nani but hides her love from him.
A young, naive boy named Billy Forrester (Luke Benward) has a weak stomach and vomits easily. He and his parents, Mitch (Tom Cavanagh), Helen (Kimberly Williams-Paisley), and his little brother, Woody (Ty Panitz), have just moved to a new town. Billy tells his mother that he doesn't want to go to school because he will be "the new kid". She assures him that he will make friends and everything will be okay. At school, however, he becomes the target of the school bully, Joe Guire (Adam Hicks), his two "toaders" named Plug (Blake Garrett) and Bradley (Philip Daniel Bolden), and the rest of his gang: Benjy (Ryan Malgarini), Techno-Mouth (Andrew Gillingham), Twitch (Alexander Gould), and Donny (Alexander Agate). They rudely stare at him and call him "Billy F." (which is how his name is written on his lunch box). Plug and Bradley steal his lunch box. He sits behind Erykka Tansy (Hallie Eisenberg), an unusually tall girl whom people make fun of (calling her "Erk").
Kiryu is undergoing repair modifications after its battle with Godzilla. Prime Minister Hayato Igarashi accepts Lead Scientist Yoshito Chujo's choice to replace the Absolute Zero Cannon with a powerful Tri-Maser.
Endless warfare and environmental pollution have resulted in the frequent appearance of monsters. The Earth Defense Force (EDF) is established. Mutant humans with extraordinary physical capabilities are discovered and are organized into an EDF troop called the M-Organization. Their main opponent is Godzilla, first sighted in 1954. After repeated battles, Godzilla is captured in a crevasse at the South Pole and buried under an avalanche of ice. The EDF ship Gotengo, commanded by Captain Gordon, battles and destroys Manda but in the process, the ship is wrecked and Gordon is dismissed from the EDF. At M headquarters, mutants Ozaki and Kazama spar before their next mission.
The prologue of the film acknowledges the events of the first Godzilla film, while inventing its own timeline, explaining 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 Prefecture. After this, a section of Japanese Self Defence Force was dedicated to fight Godzilla, and was called G-Graspers. In 1996, clean plasma energy replaced nuclear energy, however this did not deter Godzilla from attacking. Plasma energy is also banned, due to the fact that Godzilla attacked the original plasma energy reactor.