The game has three different fighting styles: Average, a system reminiscent of Street Fighter Alpha that fills up and acts normally allowing for level 1 and 2 supers; Counter, which works by charging up your power gauge and allowing Level 2 supers when your health is low in conjunction with the full bar, exactly like The King of Fighters '94-'95 and the Extra Modes of '97-'98; and Rush which is a blend of the Versus and KOF '96-present (known as Advanced in '97 and '98) systems, but locks out level 2 supers. The single player Tournament mode could be played in a standard single character style, as well as in Marvel vs. Capcom-style Tag Teams or KOF-style three-on-three battles. In Tourney mode, the player would fight a certain rival halfway through, then a team of three clone fighters, a tag-team of Geese and Bison and finally, either Evil Ryu or Orochi Iori (only if you beat your rival beforehand, though), for a whopping total of nine stages.
It also features Olympic mode, a collection of minigames, which included many SNK and Capcom characters such as the Red Arremer and Arthur and Marco, Fio and Mars People. This mode allowed players to unlock extra super attacks for the main cast. Beforehand you picked either the SNK side or Capcom side and would be managed by either Rimururu or Karin Kanzuki respectively.
- Fatal Fury: Terry Bogard, Mai Shiranui, Geese Howardnote
- Art of Fighting: Ryo Sakazaki, Yuri Sakazaki (unlockable)
- The King of Fighters: Kyo Kusanagi, Iori Yagami, Leona Heidern, Orochi Iorinote
- Psycho Soldier: Athena Asamiya
- Samurai Shodown: Haohmaru, Nakoruru
- The Last Blade: Akari Ichijou (unlockable)
- Street Fighter: Ryu, Ken Masters
- Street Fighter II: Guile, Chun-Li, Zangief, M. Bisonnote , Akuma (unlockable)
- Street Fighter Alpha: Sakura, Evil Ryunote
- Darkstalkers: Morrigan Aensland, Felicia, Baby Bonnie Hood (unlockable)
This game shows examples of:
- All There in the Manual: Despite the game giving a healthy amount of in-story for each character via Dialogue Trees and cutscenes, they do have their motivations to join the tournament, which are listed in the game's Japanese official site (only for the starting characters, though).
- Assist Character: When you perform Morrigan's Level 2 Darkness Illusion, Lilith appears to surround your opponent. Similarly, B.B. Hood's Level 2 Cool Hunting replaces the giant riflemen with a pair of laser-firing Huitzil.
- The Cameo:
- This game won't function on a regular Neo Geo Pocket, but attempting to play it on that console instead gives you cute cameo images like K' and Alex staring down each other, King and Chizuru smiling and giving you a heartfelt apology, an adorably despondent Xiangfei playing a Neo Geo Pocket while Chun-Li does her taunt, Kaede playing with Lilith Aensland and even Kyo in his KOF 99 outfit (he wears his school uniform in game) teasing Iori about needing an NGPC to play the game.
- Just before a player reaches the fight with their rival, they'll be attacked by either Vega or Billy Kane, who will then be easily dispatched by the rival in question. They also appear in Geese vs. Bison intros.
- The Olympic mode is already full of cameos (as mentioned above), but as a bonus, Lord Raptor can be seen jamming on his guitar during the "Cat Walk" event.
- Beating an Olympic event with Ryu will cause the record screen to show a poduim with Bison and Sagat while the first position is vacant, as a nod to his Street Fighter II ending.
- Cloning Blues: If you have Ryu in a team led by an SNK character, you'll fight Evil Ryu at the end. When he notices this during the cutscene before the boss fight, Geese tells him that the other Ryu you'll be fighting is a clone with an artificial form of Satsui no Hado implanted in his brain. Same goes for Iori if your captain is from Capcom. Oh, and if you play with Geese and/or M.Bison, the one(s) at the end will be a clone(s), too.
- Cloud Cuckoolander: Akari has shades of this.What am I doing? Who am I?
Am I a butterfly dreaming...
Yah! I'm freaking myself out here!
- Continuity Nod: Ryo suggests bringing Kyokugen Karate to Brazil in his ending (referencing where Marco Rodriguez/Khushnood Butt from Garou: Mark of the Wolves comes from and who he learned it from). In fact, the entire idea to build the dojo in Brazil came from Takuma, who wanted to use the tournament's prize money for that end.
- Dumb Is Good: Felicia never realized that her first "friend" (Akari Ichijo) actually wanted to capture and keep her as a pet, but only changed her mind after realizing Felicia's feeding expenses would cost a fortune.
- In Akari's ending, Felicia actually starts to figure out what Akari's up to and beats a hasty retreat.Akari: Oh... Nice kitty! You're all right for a freak! So, what else do you want. Hey, freakie?!
Felicia: ......... Bye... (flees, as Akari just stares in awe)
- In Akari's ending, Felicia actually starts to figure out what Akari's up to and beats a hasty retreat.
- I Just Want to Have Friends: The entire reason why Felicia's in the throwdown.
- Luck-Based Mission: Oddly enough, unlocking characters is this. Usually when you beat the game you see a bunch of blocks and random blocks disappear to reveal a hidden fighter's silhouette. If all the blocks are gone you unlock that fighter. Problem is, its entirely random which blocks it'll make disappear, and the game often decides to hit spaces whose blocks had already been eliminated, even if you play on higher difficulty levels, which break more blocks. It's suggested that not following a pattern in choosing characters can help speed up the process; the blocks the game shatters for you are still decided at random, though.
- However, if you have a Card Fighters Clash save and link it with this game, the unlocking system becomes much less painful. It's even possible to achieve a two-way 100% Completion if you've collected enough Versus points in the Olympic events, because the amount of content you unlock in Card Fighters depends on how many Versus you transfer from Match of the Millennium, and the fuller your deck, the more secret chars you may have at your disposal.
- Nostalgia Level: With the exception of Dotonbori (which is a real location in Osaka) and the underground lab where the final levels take place, all other arenas are classic stages from both companies' games.
- Only in It for the Money: With a majority of the cast consisting of humans, coupled with some of her dialogue, this seems to be B.B. Hood's raison d'etre in this game, rather than being in it just for the slaughter as in Vampire Savior.
- Original Generation: Sort of. While Evil Ryu and Orochi Iori are familiar to everybody, in this game they're the result of Bison and Geese's genetic tampering on said captured fighters rather than their dark sides coming to surface on their own. Plus, if you're actually playing with Ryu and/or Iori, the ones you fight are outright said to be clones.
- Pet the Dog: If you lose your rival battle (between stages 4 and 5), you get a special quote from your leading character's rival. Pretty much all of them wish you luck for the next stage (which, in-game, is the tournament's final match). Even those who would have no reason to do so:B.B. Hood: (to Yuri) Nice fight! Go nuts tomorrow!
Iori: (to Akuma) Butch up, trash! Win the finals!
Geese: (to Bison) I won't kill you! Do your job!
- Take That, Audience!: The player can "talk" with their Olympic mode managers. Sometimes when talking with Rimururu, she'll ask you what you want to do later in your life and one option is to "marry Nakoruru." Choosing this option however makes her gape at you, remind you that Nakoruru isn't real and write you off as a weird pervert.