The film opens with the outbreak of a war in the previously peaceful kingdom of Wredpryd. Count Ferdinand is the inventor of a new submarine who is assigned to command the new ship in battle. The King of Wredpryd orders the Count to sink the "ProPatria" ("for my country"), a civilian ship that is believed to be carrying munitions as well as civilian passengers. In his mind's eye, the Count sees a vision of what would happen if he sent a torpedo crashing into the liner, and he recoils. He refuses to follow his orders, saying he is "obeying orders -- from a Higher Power." Realizing his crew will carry out the orders, the Count fights with the crew and blows up his submarine, sending it to the bottom of the sea.
The legendary empire of the lost continent of Mu reappears to threaten the world with domination. While countries unite to resist, an isolated World War II Captain has created the greatest warship ever seen, and possibly the surface world's only defense.
In 1899, men dressed as German soldiers, using a large armored vehicle and wielding machine guns, attacked the Bank of England and stole Leonardo da Vinci’s layouts of Venice’s foundations. Shortly after, led by their leader the “Fantom”, men dressed as British officers, again using highly advanced technology for the time, kidnapped German scientists and destroyed a factory, causing tension between the United Kingdom and Germany, which could lead to an international war. Sanderson Reed (Tom Goodman-Hill) of the British Empire ventures to Kenya, visiting a Gentleman's club to recruit world-renowned hunter and adventurer Allan Quatermain (Sean Connery). Quatermain, retired and mourning the loss of his son after his last adventure, has no interest in serving the British Empire further. After armed men attempt to assassinate Quatermain, he is left with no-other choice but to agree to go with Reed to London and meet with Reed's superior officer to help keep the threat of a war from spilling into Africa.
Martin, CEO of Tri-Oceanic Corp, hires geologist Steven Beck to command an undersea mining operation for six months. While working outside their deep sea station in a pressure suit, one of the crewmembers, Sixpack, discovers a Soviet shipwreck, Leviathan.
Pat Fairlie is out of the Navy now and travels to Jamaica to renew acquaintance with Ena Dacey, an old flame. Ena lives on a stately sugar plantation with her brother, Todd, and their mother.
Mike and Tony Petrakis are Greek American father and son sponge diving entrepreneurs who find themselves in competition with the Rhys family, WASP fishermen who are prepared to resort to violence and even murder to maintain their established fishing grounds off the Gulf Coast of Florida. Run-ins between the two clans lead to an exchange of threats and all-out brawls. Further complications ensue when Tony Petrakis meets Gwyneth Rhys, and the two fall in love.
In the near future, weapons master James McCullen (Christopher Eccleston) has created a nanotech-based weapon - nanomites designed to devour metal and other materials, capable of destroying anything from tanks to cities. The nanobots can only be stopped by activating the kill switch. His company M.A.R.S. (Military Armaments Research Syndicate) sells four warheads to NATO, and NATO troops led by American soldiers Duke (Channing Tatum) and Ripcord (Marlon Wayans) are tasked with delivering the warheads. Their convoy is ambushed by the Baroness (Sienna Miller), whom Duke recognizes to be his ex-fiancee Ana Lewis. Duke and Ripcord are rescued by Scarlett (Rachel Nichols), Snake Eyes (Ray Park), Breaker (Saïd Taghmaoui) and Heavy Duty (Adewale Akinnuoye-Agbaje). They take the warheads to The Pit, G.I. Joe's command center in Egypt, and upon arriving rendezvous with the head of the G.I. Joe Team, General Hawk (Dennis Quaid). Hawk takes command of the warheads and excuses Duke and Ripcord, only to be convinced to let them join his group, after Duke reveals that he knows the Baroness.
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 crew of an American submarine are on a reconnaissance mission photographing Japanese installations through a periscope camera. When attacked by the Japanese (with similarities to the USS Perch) the submarine is scuttled and the crew is captured. Tortured by the Japanese, with the help of British and Australian prisoners the crew makes an escape bid to get their information to the Allies. The film ends with footage of the Battle of the Coral Sea that according to the film was made possible through the information brought back by the submariners.
Gibbie Gibson (Donald Pleasence) has discovered a World War II-era plane wreck in the mountains of New Zealand. When his discovery gets around town, Gibson, his daughter Sally (Lesley Ann Warren), and his lodger Barney Whitaker (Ken Wahl) find trouble from a group of treasure hunters led by a Mister Theo Brown (George Peppard), who are intent on finding the cache of money they believe is on the wreck.
A World War II-era German submarine missing for 20 years is retrieved in the Bahamas by diver Mark Brittain, hired by the wealthy Rosa Lucchesi and her partner, Vic Rossiter, who have been searching for Spanish galleons.
L'année 1886 est marquée par des événements mystérieux survenus en mer : une créature étrange et gigantesque, que les meilleurs scientifiques ne peuvent identifier, s'attaque aux navires en transperçant leur coque.
A small group of British sailors stationed on a Scottish island engaged in top-secret research on a new and dangerous torpedo are joined by a US Navy scientist, Lt. Brad Bradville (Gene Kelly), and his assistants. When several tests of the weapon fail, and men are killed, tensions within the group mount. Bradville must prove that the torpedo can work and win over the British, especially Lt. Rogert Wharton (John Justin), before the Admiralty pulls the plug on the project.
On Santorini island, Greece, a wedding is interrupted by a strong earthquake. The earthquake uncovers the Luna Temple, built by Alexander the Great to house his most prized treasures. Among these treasures is a glowing orb with a pattern resembling a code etched into it. Lara (Angelina Jolie) finds this orb; but it is stolen by the crime lord Chen Lo (Simon Yam). Lara only just manages to escape with a strange medallion, while her two companions are killed by Chen's men.