*SPOILER* *Warning, this tells the Entire Plot of both Metal Gear Solid and Metal Gear Solid 2*
Metal Gear Solid 2: Sons of Liberty is the newest incarnation of the Metal Gear series that was created, produced, and directed by Hideo Kojima. The game opens 2 years after the previous Metal Gear Solid with Solid Snake, the hero of the first MGS. During the first MGS, Solid Snake was sent into Alaska by FOXHOUND (a government agency), to infiltrate a development site of the Metal Gear, a bipedal robot armed with nuclear capabilites. While infiltrating "Shadow Moses," Snake finds out that he is merely a clone of the legendary mercenary Big Boss and that another clone, Liquid Snake has taken control of Metal Gear. After destroying Liquid and the Metal Gear, Solid escapes Shadow Moses to go into retirement.
Between the two years that has passed between the first and second, the United States Marines developed a new type of Metal Gear, Metal Gear RAY, which happens to be amphibious. After catching wind of this, Snake boards the USS Liberty in New York harbor, which contains RAY. While boarding however, a Russian army also infiltrates the ship with Revolver Ocelot (MGS veteran) heading the operation. When Snake shows himself to Ocelot, Ocelot's arm animates, revealing the remnants of Liquid. Liquid takes over Ocelot, takes RAY, and destroys the Liberty. Snake escapes.
Two years later, the game opens with Raiden, a white haired rookie who is also sent by FOXHOUND. After the tanker went down, crude oil spilled all over New York Harbor. The government created the Big Shell, a treatment facility. While on a tour, the President gets captured by a terrorist group, thus the reason why Raiden was sent in. After disarming C4 placed on the struts of the Big Shell. Raiden meets with the President. The President reveals that this whole operation is not for the terrorists to capture him. Actually, the Big Shell is a storage facility for the new US Navy-brand Metal Gear Ray. In addition, the Prez reveals information on the Patriots, a shadowy group of 12 men that control every aspect of life in America. They control all information and if they control the information, they control everything. The Prez wanted to become a Patriot, and decided to help the terrorists. The leader of the terrorists, however, is Solidus Snake, the third clone of Big Boss. He wants to "free" the American people by detonating a nuclear device over Manhattan, thus creating an electronic disturbance. From there, he would create a nation free of the Patriots.
The Prez reveals one more thing. There is a new Metal Gear: Metal Gear Arsenal. A floating tank, basically, it houses several RAYs and it would help Solidus with his plans. Raiden now has to get rid of Arsenal before it can knock out Manhattan. Raiden gets the virus that is needed; in Arsenal, it also turns out that his semi-partner Lt. Grade Pliskin, is actually Solid Snake himself. While in Arsenal, Raiden gets 2 pieces of news. Firstly, Raiden's past happens to be one of a child soldier. He was trained by Solidus, but as an adult, he refused to acknowledge it. Secondly, Raiden becomes aware of the S3 program, or Solid Snake Simulation. The S3 was made to create identical clones of Solid Snake to be used on the battle field. The entire Big Shell Operation was used to simulate the Shadow Moses incident, down to the last detail. Raiden was chosen because he refuses to acknowledge his past. As Raiden gets to the top of Arsenal, he meets Solidus, his adoptive father and Ocelot, who is being controlled by Liquid Snake. Ocelot/Liquid, in fact, worked for the Patriots all along and revealed the final piece of the puzzle.
The S3 program does not mean Solid Snake Simulation. It means Simulation for Social Sanity. All of Raiden's mission was a program to control how he felt, thought, and acted. Every emotion was planned out by the Patriots, even though they were real. Ocelot/Liquid escapes in a stolen RAY as Arsenal crashes into Manhattan. In the final showdown, Raiden and Solidus must fight, even though Solidus wanted to free the people and the fight was according to the Patriots' plans. At the end of MGS2, with Solidus defeated, we see Snake comforting Raiden and offering him a new life. Raiden accepts and the game ends.