The game takes place five years after the events of The King of Fighters XI and is the last game of the third story arc that started in The King of Fighters 2003. The fighter Ash Crimson has absorbed the powers from two of the descendants of the clans who sealed the Orochi away 1,800 years ago, Chizuru Kagura and Iori Yagami, while Kyo Kusanagi is to be his last victim. As his former comrade, Elisabeth Blanctorche, prepares to stop him, fighters receive an invitation to another King of Fighters tournament hosted by a person labelled as "R". The tournament is sponsored by a woman Rose who is being controlled by "Those From The Past", the organization behind the two prior tournaments that has been trying to break Orochi's seal with Ash acting as their agent.
When the winning team reaches the game's end, Saiki, the leader of "Those From The Past" puts his work into motion. Saiki intends to use the energy expended by the winning team to enable him to cross time, killing his own subordinate just to face the champions. However, as the fight rages, Botan notes that the gate that links them to the past is starting to close despite the battle. Before Saiki can act, he is ambushed by Ash who kills him and who steals his power. It is revealed then that, while Ash was enlisted by Saiki to obtain the Three Sacred Treasures to power the time gate, Ash had no intention of helping Saiki. Ash is suddenly overtaken by Saiki's persona, facing the champions of the tournaments. Saiki is defeated in the gate but persists on crossing over to the past, believing it means nothing since he can return to the past and then cross the gate again to attempt his plan anew. However, Ash halts his attempt and allows the gate to close, leaving Saiki trapped in the present. With Ash being descendant of Saiki, he denies Saiki's existence in the past and forces his own existence to cease. As Ash vanishes from the living world, the flow of time resumes. In the epilogue of the Story Mode, Chizuru and Iori recovers their powers. The remaining members of Saiki's group leave. As it appears everybody forgets Ash's existence, Elizabeth remains emotionally destroyed as she still remembers their childhood.
