MAIN STORY
The plot of Chaos Theory sees a return to the original Splinter Cell's theme of information warfare, with Sam on the trail of the Masse Kernels used by Georgian President Kombayn Nikoladze to attack America's infrastructure. The main focus in this game is Japan, North Korea, and South Korea.
The main focus of the game takes place in East Asia, 2007, with tensions running high between China, North Korea, and Japan, following Japan's formation of an Information Self Defense Force (I-SDF) (an event mentioned in a news report in Pandora Tomorrow). Considering this to be a violation of the Post-World War II Constitution, Chinese and North Korean forces establish a blockade in the Yellow Sea against Japanese shipping. Because Japan and the I-SDF are allies of the US and Third Echelon, the U.S. dispatches its most advanced cruiser, the USS Clarence E Walsh, to the Sea of Japan. The US hopes this show of strength will get China and North Korea to back down.
Meanwhile, in a seemingly unrelated incident, Sam is dispatched to locate Bruce Morgenholt, a missing computer programmer who was captured by a Peruvian separatist group called "The People's Voice", led by Hugo Lacerda, and worked on deciphering Phillip Masse's algorithms. Masse, whom Sam assassinated in the original Splinter Cell, was a genius far ahead of his time, and the algorithms he used to launch his attacks on America have been extensively studied by the UN. The resulting Masse Kernels are being touted as the superweapon of the 21st century. Sam is tasked with making sure they do not fall into the wrong hands.
Sam arrives too late to prevent Morgenholt's death. He is also unsuccessful in stopping the release of the Masse Kernels. Sam is told to go on board the Maria Narcissa to kill Hugo Lacerda and track the weapon deliveries so they can find out who they are dealing with. After completing the mission, and a mission in a Panamanian bank, unknown parties use the algorithms to black out Japan and the Eastern Seaboard, including New York City. Japan has previously suffered similar attacks that crashed its economy, and Admiral Otomo of the I-SDF contacts Third Echelon and warns them that North Korea and China are probably responsible. Meanwhile, following a lead discovered in a bank in Panama, Sam travels to New York to investigate Abrahim Zherkhezi, a man who worked with Morgenholt on Project Watson. He finds that Displace International, owned by Douglas Shetland is protecting him. He breaks into the Displace offices and learns of one Milan Nedich, later identified as "Milos Nowak", a Bosnian war criminal. Fisher finds that Nowak secretly relocated him to Hokkaido.
Sam travels to Hokkaido and meets with Shetland, who claims that Nedich is clean. Regardless, Fisher infiltrates the hideout that Zherkezi is being held in. There, Sam kills Nedich, and witnesses Shetland murdering Zherkezi. Shetland escapes and goes underground.
Meanwhile, the American show of force backfires when the Walsh is sunk by a North Korean anti-ship missile on July 4, initiating a war between North Korea and South Korea/United States. Since North Korea claims the missile was launched unintentionally, Sam is sent to the Korean peninsula (including the South Korean capital city of Seoul), to determine if North Korea is truly responsible for sinking the Walsh, or if the Masse Kernels are involved. (Note that the sinking of the Walsh and the U.S.-North Korea war is the plot for the PlayStation 2 and Gamecube versions of Ghost Recon 2.)
Sam eventually learns that the entire war has been orchestrated by American private security corporation Displace International. Displace used the Masse Kernels gained from Zherkhezi to hijack North Korea's missile systems, and sink the Walsh, in order to draw the U.S. into a war from which Displace could profit through its status as a leading American PMC. Sam also realizes the mastermind behind the entire plot is none other than his old war comrade and friend, Douglas Shetland. Ultimately, Third Echelon sends him to spy on a meeting between Shetland and Shetland's unknown accomplices, who shockingly turn out to be the I-SDF. At the meeting, the I-SDF betray Shetland, and a firefight subsequently breaks out between Shetland's soldiers and I-SDF assault troops. Amidst the chaos, Sam pursues Shetland to the roof, where, after a tense Mexican standoff, Sam kills Shetland.
Even after Shetland's death, one loose end remains. Admiral Otomo of the I-SDF has acquired a copy of the Masse Kernels from Shetland, and attempts to return Japan to Imperial rule by blackmailing the Japanese government officials and senior JSDF officers. He threatens to use the algorithms to launch a North Korean missile against a Japanese city. Because North Korea would be supported by China, and Japan would be backed by the U.S, the incident would spark World War III. Although Otomo's loyalist I-SDF soldiers manage to fight off the JGSDF commandos sent to stop him, Sam infiltrates the I-SDF's lowest levels and manages to put an end to Otomo's plans, possibly after being captured and interrogated by, and escaping from, I-SDF troops. Otomo attempts to commit seppuku, but Sam saves his life and captures him. Otomo stands trial at the UN and takes full responsibility for the entire Korean crisis, returning stability to the Far East.
CO-OP STORYLINE
Two NSA operatives start off the campaign with basic training, introducing the players to the game-play elements of the cooperative play. Uncharacteristically, they are given similar weapons as Sam Fisher, boosting them to lethal status. After passing training, the operatives are sent to Panama, tying up the loose ends and clues that Sam Fisher picked up from Hugo Lacerda. The Operatives interrogate the Vice President of the bank and sifted through all available records to find out that other than aiding Hugo Lacerda, the bank had aided North Korea in smuggling nuclear and chemical weapons through Panama. A name, Jong-Pom-Chu appears in the records. Shortly after completing the mission, Lambert promotes the operatives into "Splinter Cells-in-Training."
The action then picks up in a war-torn South Korea, with the operatives trying to locate Jong-Pom-Chu. The operatives were tasked to destroy any anti-air vehicles and look for the Korean scientist. Unfortunately he was moved during the mission, and Sam Fisher needed to interrogate a North Korean Special Forces soldier to find out where. The operatives dismiss the idea that he is another Splinter Cell, as they believe they are the first. The trainees eventually evacuate Jong in a truck.
The operatives were then sent to a chemical missile bunker in North Korea, sometime after the end of the single-player campaign. The operatives were tasked to investigate what type of weapons development Jong was involved with. The operatives then later found out that the North Koreans were developing viral weapons, using monkeys as the guinea pigs. Lambert ultimately gives the order to create an anti-virus and retrieve a viral sample from a warhead. The operatives managed to exfiltrate by boat.
The operatives were then placed in New York City, tasked to disarming bombs in the train systems planted by rogue North Korean personnel attempting to recover a virus stashed in a locker. With help from Jong, the operatives recover the virus and manage to thwart the investigating North Korean soldiers.
The operatives are sent on a return trip back to North Korea, this time investigating a nuclear power plant. The operatives were tasked to finding out who helped Kim, the leading North Korean officer behind the weapons fiasco.
The operatives' final mission ends up at the United Nations Headquarters in New York, putting a stop to a now-desperate Kim's plan to blow up the building before an important meeting takes place. The operatives kill Kim and disarm the bomb the North Korean agents planted.
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