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.
The British spy boat St Georges, which holds the Automatic Targeting Attack Communicator (ATAC), the system used by the Ministry of Defence to communicate with and co-ordinate the Royal Navy's fleet of Polaris submarines, is sunk after accidentally trawling an old naval mine in the Ionian Sea. MI6 agent James Bond, code name "007", is ordered by the Minister of Defence, Sir Frederick Gray and MI6 Chief of Staff, Bill Tanner, to retrieve the ATAC before the Soviets, as the transmitter could order attacks by the submarines' Polaris ballistic missiles.
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.
After MI6 agent James Bond, 007, fails a routine training exercise, his superior, M, orders Bond to a health clinic outside London to get back into shape. While there, Bond witnesses a mysterious nurse named Fatima Blush giving a sadomasochistic beating to a patient in a nearby room. The man's face is bandaged and after Blush finishes her beating, Bond sees the patient using a machine which scans his eye. Bond is seen by Blush and an attempt is subsequently made to kill him in the clinic gym, but Bond manages to defeat the assassin.
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.
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.
James Bond—MI6 agent 007 and sometimes simply "007"—attends the funeral of Colonel Jacques Bouvar, a SPECTRE operative (Number 6). Bouvar is alive and disguised as his own widow, but Bond identifies him. Following him to a château, Bond fights and kills him, escaping using a jetpack and his Aston Martin DB5.
Seventeen-year-old Joshua "Josh" McGuire (Rhys Wakefield), expedition bank-roller Carl Hurley (Ioan Gruffudd) and his girlfriend, Victoria "Vic" Elaine (Alice Parkinson), travel to the Esa'ala Cave, an underwater cave exploration site in Papua New Guinea. Josh's father, Frank (Richard Roxburgh), a master diver, has already established a forward base camp at a lower level inside the cave, where the team has been exploring for weeks. As Josh begins to advertise his disdain for his father and his opinions about cave exploration, the team below prepares to dive into an unexplored area of the system.
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.
Fisherman Matt Boyd (Richard Dreyfuss) is fishing in Lake Victoria when a small earthquake hits, splitting the lake floor and causing a whirlpool. Boyd falls in, and is ripped apart by a shoal of piranhas that emerge from the chasm.
At Aquatica, a remote former submarine refueling facility converted into a laboratory, a team of scientists is searching for a cure for Alzheimer's disease. Fluids from the brain tissue of three Mako sharks are being harvested as a cure for Alzheimer's. Unknown to the other scientists, Dr. Susan McAlester (Saffron Burrows) has violated the code of ethics and has genetically engineered the sharks to increase their brain size, but this has the side effect of making the sharks smarter and more dangerous.