It has been a while since the existence of the mysterious secret syndicate NESTS was brought to light. Since then, however, their presence still remains a mystery and they've kept their activities well under wraps.
Meanwhile, in contrast to NESTS seeming lack of action, an increase in terrorist activities throughout the world has been taking place. Heidern and his band of mercenaries have determined that these events are the work of K' and Maxima.
Heidern and his band quickly begin pursuit of these two, but just as they begin their efforts, the invitations for the latest KOF tournament are sent....!
The fighters ready themselves for the tournament to begin in various venues throughout the world.
Most remarkable among the invited teams is one in which K' and Maxima are listed as members!
Moreover, NESTS whip into the second phase of their project, as if summoned into action by the two "terrorists."
Is the beginning of NESTS's activities a mere coincidence? Or, could it be...?
Once again a feeling of impending conflict stifles the air, and the curtain on the latest King of Fighters is about to rise...!!!
於《格鬥天王'2000》仍然由NESTS舉辦賽事，主角K'、麥克斯與紅丸、真吾各自組隊參賽，K'兩人與特務VANESSA(凡妮莎)及RAMON(拉蒙)組成隊伍，紅丸兩人則與紅丸好友同為特務的SETH(賽斯)以及為尋人參賽的LIN(麟)組成新隊伍。比賽期間組織專門為剋制K'所研究的女改造人綽號「Anti K'」使用冰能力的KULA DIAMOND(庫拉.戴雅門度)突然出現並與K'對決，結果K'擊敗了庫拉，其保護人之一DANNA(黛安娜)帶同古娜及其機械同伴卡蒂．戴雅門度(CANDY DIAMOND)離開。大賽結束後，意圖背叛組織並利用組織兵器控制世界的CLONED.Zero（複製零）現身，庫拉與組織高層兼其保護人DANNA(黛安娜)及Foxy(霍斯)合力阻止C.Zero背叛NESTS組織的計劃，同時海迪倫上校亦於另一方面阻止其野心。阻止過程中庫拉的機械同伴卡蒂，為保護庫拉而導致全身破碎失去動力，庫拉立下決心要修復令卡蒂重現。另一方面K'等人阻止並擊敗C.Zero，成功解救一次危機，CLONED.Zero（複製零）則被組織以背叛之罪處決。