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.
In 2055 Chicago, the Time Safari company offers the ability for people to hunt dinosaurs in the past via time travel technology. Because of the dangers of interferring with the time line, the company's activities are is vocally attacked by Sonia Rand, the developer of the time machine software TAMI, who feels scorned for not receiving credit and fears they may alter the past through their activities.
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.
In 1992, journalist Kenichiro Terasawa (Kosuke Toyohara) is writing a book about Godzilla and learns about a group of Japanese soldiers stationed on Lagos Island in the South Pacific during World War II. They were unintentionally saved from a group of American soldiers by a mysterious dinosaur known as "Godzillasaurus" in February 1944. In 1954, the island was destroyed by a hydrogen bomb test and the radiation from the bomb mutated the dinosaur into Godzilla.
In New York Harbor, Carl Denham, famous for making wildlife films in remote and exotic locations, charters Captain Englehorn's ship Venture for his new project, but he is unable to secure an actress for a female role he reluctantly added. Denham searches the streets of New York for a suitable woman. He meets penniless Ann Darrow and convinces her to join him for the adventure of a lifetime. The Venture quickly gets underway. The surly first mate, Jack Driscoll, gradually falls in love with Ann. After weeks of secrecy, Denham finally tells Englehorn and Driscoll that their destination is Skull Island, an uncharted island shown on a map in Denham's possession. Denham speaks of something monstrous there, a legendary entity known only as "Kong".
In Edinburgh, Scotland, in 1880, Professor Sir Oliver Lindenbrook (James Mason), a geologist at the University of Edinburgh, is given a piece of volcanic rock by his admiring student, Alec McEwan (Pat Boone). Deciding that the rock is unusually heavy, Lindenbrook, mostly thanks to the carelessness of his lab assistant, Mr. Paisley (Ben Wright), discovers a plumb bob inside bearing a cryptic inscription. Lindenbrook and Alec discover that it was left by a scientist named Arne Saknussemm, who had, almost 300 years earlier, found a passage to the center of the Earth. After translating the message, Lindenbrook immediately sets off with Alec to follow in the Icelandic pioneer's footsteps.
News reporter Ichiro Sakai and photographer Junko Nakanishi take pictures of a wreckage caused by a typhoon. They uncover a strange, bluish-gray object in the debris, not knowing its significance. Later that day, a giant egg is discovered on the shore. The local villagers salvage it, and an entrepreneur of Happy Enterprises named Kumayama buys the egg from the local villagers. Instead of letting scientists study the egg, Kumayama wants to make it into a large tourist attraction. Later, Sakai and Nakanishi are informed that the strange object they found is extremely radioactive. (It is later hinted that this is a skin particle from Godzilla.
Young urban professionals Jesse (Arye Gross) and his girlfriend Kate (Lar Park Lincoln) move into an old mansion that has been in Jesse's family for generations. They are soon joined by Jesse's goofy friend Charlie (Jonathan Stark), who brought along his diva girlfriend Lana (Amy Yasbeck), in the hopes of being discovered by Kate, who works for a record company. Jesse has returned to this old family mansion after his parents were murdered when he was a baby. While going through old things in the basement, Jesse finds a picture of his great-great grandfather (and namesake) in front of a Mayan temple holding a crystal skull with jewels in the eyes. In the background is a man Jesse learns is Slim Razor, a former partner of his great-great grandfather turned bitter enemy after a disagreement over who would get to keep the skull.
The film opens with a trio of young bluebirds harassing their youngest sibling, Buster (Blaze Berdahl). As Buster leaves his family, he meets an intelligent orange T. rex named Rex (John Goodman) playing golf. He explains to Buster that he was once a ravaging dinosaur, and proceeds to tell the story of how he came to become what he is today.
Akoba (Robert Brown) leads a hunting party into the hills to search for prey. One member of the tribe traps a warthog in a pit, and then Akoba's son Tumak (John Richardson) kills it. The tribe brings it home for dinner and Tumak is later banished to the harsh desert because of a fight over a piece of meat with Akoba. After surviving many dangers such as a giant iguana, ape men, Apatosaurus and a giant spider, he collapses on a remote beach, where he is spotted by "Loana the Fair One" (Raquel Welch) and her fellow fisherwomen of the Shell tribe. They are about to help him when an Archelon (which is three times the size of the actual prehistoric Archelon) makes its way to the beach. Men of the Shell tribe arrive and drive it back into the sea. Tumak is taken to their village, where Loana tends to him. Scenes follow emphasising that the Shell tribe is more advanced and more civilized than the Rock tribe. They have cave paintings, music, delicate jewellery made from shells, agriculture, and rudimentary language – all things Tumak seems to have never before encountered.
In the aftermath of Godzilla's attack on Tokyo and his later imprisonment at Mt. Mihara. a team of scientists discovers cells left in the rubble by the monster and collects them. A group of American militants takes a sample of their own. They attempt to escape with them, but are killed by a lone assassin codenamed SSS9, who steals the sample and departs. He boards a cruise liner and heads to the Republic of Saradia to deliver the cells to the Saradia Institute of Technology and Science. The president of the institute wants to use the cells to merge with genetically modified plants, hoping to transform Saradia's deserts to vast greenery and end the country's dependence on oil wells for wealth. Dr. Genshiro Shiragami and his daughter, Erika, are enlisted to aid with the ambitious project. However, a terrorist bombing destroys the institute's laboratory, ruining the cells and killing Erika.
Escaping from China with a microfilm of the formula for the mysterious "Lotus X", Lord Southmere, a Queen's Messenger, is chased by a group of Chinese spies.
Far north of the Arctic Circle, a nuclear bomb test, dubbed "Operation Experiment", is conducted. Prophetically, right after the blast, physicist Thomas Nesbitt (Paul Christian) muses, "What the cumulative effects of all these atomic explosions and tests will be, only time will tell." No sooner said, the explosion awakens a 30-foot (10 m) tall, 100-foot (30 m) long carnivorous animal known as Rhedosaurus, thawing it out of the ice where it had been held in suspended animation. Nesbitt is the only witness to the beast's awakening and is later dismissed out-of-hand as being delirious at the time of his "sighting". Despite the skepticism he persists, knowing what he saw.
King Kong, after being shot down from the World Trade Center, is kept alive in a coma for about 10 years at the Atlanta Institute, under the care of surgeon Dr. Amy Franklin (Linda Hamilton). In order to save Kong's life, Dr. Franklin must perform a heart transplant and give Kong a computer-monitored artificial heart. However, he lost so much blood that a transfusion is badly needed, and to complicate matters, Franklin says there no species of ape or other animal whose blood type matches Kong's. Enter adventurer Hank "Mitch" Mitchell (Brian Kerwin), who captures a giant female gorilla, who is dubbed "Lady Kong"; in Borneo (Mitchell theorizes that Borneo and the island from the first movie were once part of the same landmass), bringing her to the Institute so her blood can be used for Kong's operation. The transfusion and the heart transplant are a success, but Kong escapes along with the female.