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The final King of Fighters game released by SNK in its original state, The King of Fighters 2000 expands on the story and gameplay presented in The King of Fighters '99. This year's tournament is sponsored by the Ikari Warriors in an attempt to discover more about the NESTS organization, and to derail the plans of potential NESTS agents K' and Maxima. Not everything is as straight-forward as it usually is, however, and even the Ikari Warriors themselves are at risk of being betrayed from within by the end of the tournament. The King of Fighters 2000 features an improved Striker call system with the Active Striker System, which allows the player to call his Striker character in any situation, whether he is attacking or being attacked by the opponent, allowing him to use their strikers in combos. Moreover, in addition to the numerous nostalgic SNK characters returning as Another and Maniac Strikers, KOF 2000 welcomes newcomers such as Ramon, Vanessa, Seth, Lin, Hinako Shijo, and Kula Diamond.

After the incident at the previous tournament, the commander of the Ikari Team, Heidern, is determined to figure out the objective of the Nests cartel so that he can stop them from achieving their ruthless ambition. A fellow commander and long-time friend of Heidern, named Ling, tells the veteran fighter that K′ and Maxima were once operatives of Nests and that they may hold the key to locating the whereabouts of the mysterious organization. Using this information, Heidern decides to focus his efforts in using the next KOF tournament as a way to lure both K' and Maxima out so that they can be captured and interrogated into telling the authorities about the Nests cartel. Unknown to Heidern, however, Ling has his own agenda.