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.
In 1984, Soviet submarine Captain First Rank Marko Ramius (Connery) commands Red October, a new Typhoon-class nuclear sub featuring a caterpillar drive, rendering it undetectable to passive sonar. Ramius leaves port on orders to conduct exercises with the V.K. Konovalov, commanded by his former student Captain Tupolev (Skarsgård). Once at sea, Ramius kills political officer Ivan Putin (Firth), and commands the crew to head toward America's east coast to conduct missile drills.
British and Soviet ballistic-missile submarines mysteriously disappear. James Bond—MI6 agent 007—is summoned to investigate. On the way he escapes an ambush by Soviet agents in Austria, killing one during a downhill ski chase, and escaping via a Union Flag parachute. Bond learns that the plans for a highly advanced submarine tracking system are on the market in Egypt. There, he encounters Major Anya Amasova—KGB agent Triple X—his rival for the plans. They travel across Egypt together, tracking the microfilm plans, meeting Jaws—a tall assassin with steel teeth—along the way. Bond and Amasova later team up through a truce agreed by their respective superiors and identify the person responsible for the thefts as the shipping tycoon, scientist, and anarchist Karl Stromberg.
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.
In post-Soviet Russia, civil war erupts as a result of armed conflict in Chechnya. Military units, loyal to Russian ultra-nationalist Vladimir Radchenko, have taken control of a nuclear missile installation and are threatening nuclear war if either the American or Russian governments attempt to confront him.
In 1988 a US ballistic missile submarine, the USS Montana, sinks near the edge of the Cayman Trough after an accidental encounter with an unidentified submerged object. As Soviet ships and submarines head toward the area in an attempt to salvage the sub, and with a hurricane moving in, the Americans decide that the quickest way to mount a rescue is to insert a SEAL team onto the Deep Core, a privately owned, experimental underwater oil drilling platform, located 1,700 feet (518 meters) below sea level, which will serve as their base of operations. The designer of the platform, Dr. Lindsey Brigman, insists on accompanying the SEAL team, even though her estranged husband, Virgil "Bud" Brigman, is currently serving as the platform's foreman.
The story is told from the viewpoint of Lt. Werner (Herbert Grönemeyer), who has been assigned as a war correspondent on the German submarine U-96 in October 1941. He meets its captain (Jürgen Prochnow), chief engineer (Klaus Wennemann), and the crew in a French nightclub. Thomsen (Otto Sander), another captain, gives a crude drunken speech to celebrate his Ritterkreuz award, in which he openly mocks not only Winston Churchill but implicitly Adolf Hitler as well.
Lt. Commander Thomas Dodge (Kelsey Grammer), a capable yet unconventional US Navy submariner, is about to be passed over a third time for command of his own nuclear submarine because of his unorthodox methods and because of a notorious genital tattoo received after getting drunk and passing out while on shore-leave. Failure to secure a command will result in Dodge being dropped from the Navy's command program and an assignment to a desk job, and that means he will resign from the Navy. During his career, Dodge has made an enemy of Rear Admiral Yancy Graham (Bruce Dern), who strongly speaks out against Dodge's command promotion.
A alien spacecraft is discovered on the floor of the Pacific Ocean, estimated to have been there for 300 years. A team of experts, including marine biologist Dr. Beth Halperin, mathematician Dr. Harry Adams, astrophysicist Dr. Ted Fielding, psychologist Dr. Norman Goodman, and U.S. Navy Capt. Harold Barnes, are assembled and taken to the Habitat, a state-of-the-art living environment located near the spacecraft.
In 1961, the Soviet Union launches its first ballistic missile nuclear submarine, the K-19. The ship is led by Captain Alexei Vostrikov, aided by executive officer Mikhail Polenin. Polenin, the original captain, and the crew have served together for some time but Vostrikov's appointment is alleged to have been aided by his wife's political connections. During his first inspection, Vostrikov discovers the submarine's reactor officer to be drunk and asleep on duty. Vostrikov sacks the officer and orders Polenin to request a replacement. The new reactor officer, Vadim Radtchenko, arrives direct from nuclear school having just been fresh from the naval academy, annoying Polenin who thinks Vostrikov was too punitive on the former reactor officer who was competent despite his momentary lapse of judgment. Also, during the preparation period for the sub's launch, the ship's medical officer is killed when struck by an oncoming truck, and is subsequently replaced by the command's foremost medical officer, an army officer who has graciously offered himself in the submarine's time of need, but also privately admits to Vostrikov that as an army officer he has never been out to sea and suffers from motion sickness. During the K-19's official launch, the bottle of champagne fails to break when it strikes the bow; the sailors nervously glance at each other due to this customary sign of bad luck.
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).
A Russian submarine called Спрут ("Octopus") draws too close to the New England coast one morning when its captain (Theodore Bikel) wants to take a good look at America and runs aground on a sandbar near the fictional Gloucester Island, which, from other references in the movie, is located off the coast of Cape Ann or Cape Cod, Massachusetts. Rather than radio for help and risk an embarrassing international incident, the captain sends a nine-man landing party, headed by his zampolit (Political Officer) Lieutenant Yuri Rozanov (Alan Arkin), to find a motor launch to help free the submarine from the bar. The men arrive at the house of Walt Whittaker (Carl Reiner), a vacationing playwright from New York City. Whittaker is eager to get his wife Elspeth (Eva Marie Saint) and two children, obnoxious but precocious nine and half-year-old Pete (Sheldon Collins) and three-year-old Annie (Cindy Putnam), off the island now that summer is over.
The United States and the Soviet Union have both developed technology that can miniaturize matter by shrinking individual atoms, but only for a limited amount of time, depending on how small the item is miniaturized.
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.