Counter Mode increases the player's offensive strength and allows the player to use their character's Super Special Move infinitely, as well as combo that transitions from a Special Move into a Super Special Move by using a 'Super Cancellation Attack' or a 'Moving Attack'. This time, there are two powered up states the player can choose during battle depending on the button combination used. Instead, the game has a single playing style modeled after the Advanced mode from the previous game, where the player fills their power gauge by attacking the opponent or performing special moves.

The selectable fighting styles, Advanced and Extra, from KOF '98 are gone. A striker can only be summoned a limited number of times during a single match, which is determined by the number of 'Strike Bombs' at the bottom of the screen. Before a match, the player chooses three of the characters to use in the actual fights, while the fourth member becomes the designated 'Striker', a character the player summons during battle to help their character out by performing one of their Special Moves against the opponent.

Instead of the three character teams from previous KOF games, each team now has four members.

Two years have passed since the last King of Fighters tournament and nobody has seen Kyo Kusanagi or Iori Yagami since they defeated Orochi at the climax of the 1997 tournament, but out of the blue, new invitations are sent out to many characters, inviting them to a brand new tournament, though this competition is more of a secretive affair than the ones in '96 and '97.

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