The game takes place in Card Tower, which consists of 21 separate floors. All the opponents on each floor have been brainwashed by MAX, to revert them back to their usual self, you have to beat them in a card battle. You have to beat everyone on a floor to advance tot he next floor of the tower. To move around the floors, you don't have direct d-pad control, instead you can select opponents on the floor and your sprite will automatically move to that opponent.
Each floors have different gimmicks to them, certain floors contain shops which allow you to purchase new packs of cards, or a a single card chosen at random. To buy cards from the shops you have to use the currency CP which you get for defeating opponents. Some floors are trading floors, you don't need to defeat anyone to advance on this floor you can just skip it completely, or you could trade cards with the AI. For most of the tower,t he levels are split up into two sides, Capcom and SNK. When you choose which side to take you can not go back and go along the other side either due to story related reasons. The only way to go along the other side is after you complete the game you can do a New Game and carry your card decks over to a new game.
ADK characters were added to the SNK side, from games like World Heroes, Aggressors of Dark Kombat and Ninja Master's Haou Ninpou-ko. Many newcomers have been added from recent games produced by both companies, such as Capcom's Dante and Phoenix Wright as well as SNK's Yuki and Nagase. Power Stone characters are absent from the game.
Almost immediately after american version was released, an unavoidable bug was discovered in the game. The bug occurs on the ninth floor of the tower, during the second play through. The game crashes after talking to an opponent named Jon, who has to be defeated in order to finish the game. On June 6th, SNK announced that the replacement cartridge would be available in stores on June 25th and began the process of implementing a recall. These cartridges have been sent by mail along with a package of 5 King of Fighters trading cards. The recall ended in January 2008.
The European version of the game didn't contain the above-mentioned glitch. Nothing unusual happened when you talk to Jon in the New Game+, and the game proceeds normally after you beat him in a card battle.