In 1868, rumors of a sea monster attacking ships in the Pacific Ocean have created apprehension and fear among sailors, disrupting shipping lanes. The United States government invites Professor Pierre M. Aronnax (Paul Lukas) and his assistant, Conseil (Peter Lorre), onto an expedition to prove or disprove the monster's existence. On board with them is the cocky master harpooner Ned Land (Kirk Douglas).
Taking place six months after the first film, Dory suddenly recalls her childhood memories. Remembering something about "the jewel of Monterey, California", accompanied by Nemo and Marlin, she sets out to find her family. She arrives at the Monterey Marine Life Institute, where she meets Bailey, a white beluga whale; Destiny, a whale shark; and Hank the octopus, who becomes her guide.
En 1944, alors que la guerre du Pacifique fait rage, deux pilotes s'écrasent sur une île inconnue. L'un est Américain, l'autre est Japonais. Alors qu'ils s'affrontent sur place, ils sont brusquement interrompus par une gigantesque créature.
As the film opens, a small boat is seen chugging through stormy seas. A giant octopus appears from the ocean and seems bent on killing the sole crew member on deck. Suddenly, the octopus releases the man and retracts its tentacles from the boat. Relieved, the sailor peers out the porthole to see Gaira, a large green man-like creature, fighting the octopus. After easily defeating it, Gaira turns his attention to the boat and sinks it.
A strange giant "sea creature" has been rampaging the seas. The American naval ship Abraham Lincoln is sent to investigate, but is rammed by "the creature" which turns out to be The Nautilus, the fantastic submarine of the enigmatic Captain Nemo, and "Rudderless, the 'Abraham Lincoln' drifts on". Then, in "A strange rescue" he guides the sub to surface under those pitched overboard and his crew take them, including Professor Aronnax, and his daughter (who are French) below through a hatch in the surface of the deck. After they pledge not to escape, Nemo shows them the wonders of the underwater world, and even takes them hunting on the sea floor.
Amidst a storm, a boat is being piloted across the South China Sea by John Finnegan (Treat Williams). With him are his crewmen Joey "Tooch" Pantucci (Kevin J. O'Connor) and Joey's girlfriend Leila (Una Damon). Finnegan has been hired to transport a group of mercenaries, led by a man named Hanover (Wes Studi), to an undisclosed location in the middle of the ocean.
The film begins when a couple disappear while having a romantic night out on a yacht near the Pacific Northwest resort community, Grave's Point. The next day, local fisherman Whip Dalton (William Petersen) finds the empty lifeboat from the missing yacht and finds a large claw stuck into the boat. Whip sends the claw to a university to be analyzed and it ends up in the hands of marine biologist Dr. Herbert Talley (Ronald Guttman), who comes to Grave’s Point claiming it is from the tentacle of a Giant squid. The island harbor master Schuyler Graves (Charles Martin Smith) tries to hire Whip to kill the squid, but he refuses, so Graves sends out Lucas Coven (Larry Drake) instead. Coven succeeds in slaying the squid and the carcass is promptly sold by Graves to Sea Land Texas owner Osborne Manning (Denis Arndt) then unknown to the fishermen the sonar that isn't being watched detects another squid. It turns out the squid is much bigger than the one they killed and instead of following the boat or attacking, it resubmerges.
A nuclear submarine on maneuvers in the Pacific Ocean, captained by Commander Pete Mathews (Kenneth Tobey), comes into contact with a massive sonar contact. The boat is disabled but manages to free itself and return to Pearl Harbor. Animal tissue of great proportions is discovered jammed in its dive planes. A man-and-woman team of marine biologists, Lesley Joyce (Faith Domergue) and John Carter (Donald Curtis), is called in; they identify the tissue as being part of a gigantic octopus. The military authorities scoff, but are finally persuaded after receiving reports of missing swimmers and ships at sea being pulled under by a large animal. Both scientists conclude the sea beast is from the Mindanao Deep, having been forced from its natural habitat by hydrogen bomb testing in the area, which has made the giant creature radioactive, driving off its natural food supply.
Mr. Tako, head of Pacific Pharmaceuticals, is frustrated with the television shows his company is sponsoring and wants something to boost his ratings. When a doctor tells Tako about a giant monster he discovered on the small Faro Island, Tako believes that it would be a brilliant idea to use the monster to gain publicity. Tako immediately sends two men, Sakurai and Kinsaburo, to find and bring back the monster. Meanwhile, the American submarine Seahawk gets caught in an iceberg. The iceberg collapses, unleashing Godzilla (who, in the Japanese version, had been trapped within since 1955), who then destroys the submarine and a nearby military base.
Yves, a fisherman, comes home after a tiring day of fishing and soon falls asleep. In his dream, he is visited by the Fairy of the Ocean, who leads him to a submarine. Yves is made Lieutenant-in-Command and sets off on a submarine voyage.
The prologue is set in Nazi Germany during the final days of World War II. A Kriegsmarine Officer, flanked by three Commandos, barges into the laboratory of a Dr. Riesendorf with orders to seize the immortal heart of the Frankenstein Monster, on which Riesendorf is busy experimenting. The heart is summarily transported by U-Boat to be passed off to their Japanese allies via the Atlantic. In the Indian Ocean, off the Maldives, the U-Boat meets up with a Japanese Imperial Navy submarine to make the exchange. They are sighted by an Allied Forces scout plane and bombed, but not before the Kriegsmarine pass the heart (contained in a locked chest) to the Japanese, who take it back to Hiroshima for further experimentation. But just as the experiments are about to begin, Hiroshima is bombed by the Allied Forces, and the heart and the experiments vanish in the atomic fireball.
The Helios 7 space probe is sent on a mission to study the planet Jupiter. While on its outward journey to the gas giant, the probe is overtaken by the Space Amoeba, an amorphous parasitic extraterrestrial. The probe returns to Earth and crashes into the South Pacific, where the Amoeba leaves the device and inhabits the body of a cuttlefish, causing it to mutate into what is called "Gezora." The tentacled kaiju begins attacking ships and islands in the area.
When young history professor Russ is called upon by his sister to execute their late mother's estate, he is reunited with boyhood friend Mike, and with his father, the charismatic leader of a New Age cult. While exploring his memories, Russ wanders into a warehouse where hundreds of names are listed on the walls. As he sleeps that night, he dreams of a stone cudgel and awakens to find a cudgel in his motel room; the town drunk warns him that it is an instrument of sacrifice. A young liquor store clerk enlists him to help find her brother, whom she believes has been taken by the cult. Russ's aunt, who has been living in an asylum, tells him that his mother left a message hidden in her house.
Ocean Beach, a seaside tourist resort, has come under attack by a giant octopus, which captures and devours human swimmers and boaters, picking the skeletons clean of flesh and bone marrow. Marine expert Will Gleason (Bo Hopkins) and crusading newspaper reporter Ned Turner (John Huston) suspect the construction of an underwater tunnel by the Trojan company, owned by Mr. Whitehead (Henry Fonda). Trojan has been using radio signals that have been "above regulated levels", somehow maddening the octopus and causing it to attack human beings. In the end, the octopus is killed by Gleason's pair of killer whales.