Time has passed since most of Southtown was decimated by the now-destroyed Zero Cannon. Another KOF tournament is being held and this time, it's hosted by the NESTS Organization, the group of antagonists behind the events of the previous two games.

K′ and Maxima return to put an end to NESTS once and for all. They are now joined by former Ikari Team member Whip and the assassin Lin formerly from Benimaru's Team, both of whom are seeking the destruction of NESTS as well. NESTS sends their own team to compete in the tournament, composed of NESTS agents Kula Diamond, K9999, Foxy, and Angel. Kyo Kusanagi joins his former teammates of Benimaru Nikaido and Goro Daimon, reuniting the original Japan Team along with Shingo Yabuki, while Iori Yagami joins a team composed of agents Seth, Vanessa, and Ramon. Yuri Sakazaki rejoins the Art of Fighting Team, while King and Mai Shiranui once again lead the Women Fighters Team along with the returning Li Xiangfei and Hinako Shijo. Heidern also makes his KOF return, taking Whip's place in the Ikari Team, while Kim Kaphwan '​s young student May Lee takes over Jhun Hoon's place in the Korean Team, who is unable to compete due to an injury.