The story follows your character, whose gender and name is yours to choose, who's heard rumors of strange creatures fighting one another and alongside humans. Curious, the player character goes to the school computer lab to do some investigating. Naturally, a portal to the Digital World opens, and our hero quickly winds up finding the Tamer Union and becoming a Digimon Tamer.
As usual, you play a tamer who lands in the Digital World to discover it's under threat from evil. The game largely followed the format of Digimon World 3, but included a different battle style.
- Awesome, but Impractical: There are a few Digimon which can only be obtained by beating a difficult optional boss or breeding a pair of super-strong Digimon. All of them have only one form on their Digivolution lines and therefore can only be strengthened by training if they reach level 99.
- The Digivolve Disk as well. While it's impressive in the first parts of the game when a Digimon becomes Mega and destroys everything with a special attack, it's not particularly useful against other opponents.
- Boss Rush: The final quest involves defeating six bosses, then all six of them in a row, before finally letting you fight the True Final Boss. The last two bosses are FAR more difficult than the first four.
- Canon Immigrant: The game's sub-plot uses the central characters and the Big Bad and his underlings from Digimon Savers, and the game uses the Savers Agumon.
- Continuity Nod: Ancient Canyon is File Island, and Jijimon from Digimon World can be encountered on the island.
- Degraded Boss: Generally, if you beat a boss which you can raise as a Digimon and return to the area you fought it, it can be fought as part of a random battle.
- Disc-One Nuke: DotAgumon and DotFalcomon, should you choose to obtain them. High-leveled upon scan, plus they have excellent moves and traits that can carry them to the endgame
- Easily Forgiven: Cane randomly decides to go from being a bona fide Jerkass to an upstanding Tamer after the Final Boss. This second chance seems as a little unfair, seeing as all of the other renegade Tamers who didn't have the fact that they were brainwashed at the time to absolve their actions were sent back to the human world for good.
- Expy: The male version of the main character bears a striking resemblance to Ryo from the Digimon WonderSwan Series.
- Fantastic Racism: There are some Digimon who detest the Tamer Union because it's comprised of humans and Digimon working together.
- Gameplay and Story Segregation: The player can only obtain a Machinedramon outside of Digiconverting it by Digivolving it from Megadramon. The one you encounter as a villain Digivolved from SkullGreymon.
- Later in the game, Kain Digivolves a MegaKabuterimon into a GranKuwagamon (which should only Digivolve from Dinobeemon or Okuwamon), although that could be justified by how he did it.
- A few of the Digimon descriptions also don't add up, as they're adapted from other Digimon media. For example, in gameplay terms VenomMyotismon is a better fighter than MaloMyotismon, whereas the descriptions claim the opposite.
- Heroic Mime: Averted. Your character has lines and different expressions.
- Interface Spoiler: Beelzemon's defection isn't specifically mentioned, but the fact that one the requirements to Digivolve to him is 'Has befriended Beelzemon' is a bit of a clue, despite the instruction generally not meaning literally befriending. If you didn't spot him on the Digivolution chart, the fact he only occupies one space on the battlefield whereas the other Digimon he fights with occupy two to four is a clue.
- While less blatant, taking a look at the chart reveals you'll need a key item to digivolve to Antylamon, making it clear that Digimon will be important to the story.
- It Began with a Twist of Fate: If your character had chosen to ignore the rumors about the "fighting monsters that are friends with humans" he or she (you can choose your character's gender) never would have been placed on the chain of events that would culminate in saving the Digital World from destruction.
- I Want Them Alive: Towards the end of the game, Big Bad Alphamon attempts to brainwash and kidnap the player character because he needs a strong Tamer to control Chronomon.
- Light Is Not Good: Alphamon is the Big Bad.
- Mix-and-Match Critters: Kimeramon is made up of bits of various Digimon, including a character which isn't even in the game and an apparently one-of-a-kind boss you fought in a previous part of the game.
- My God, What Have I Done?: Alphamon is absolutely distraught when it seems like his rash actions have doomed the entire digital world.
- Mythology Gag: A Digimon needing a human to control the power of a legendary Digimon is very similar to the plot of Digimon V-Tamer 01, though things turned out very differently here.
- There's also the very random moment where Calumon's power is revealed towards the end of the game. This will have come as no surprise to fans who'd seen Digimon Tamers, but to anyone who hadn't will have been very confused by that plot point. But, seriously, there was NO foreshadowing whatsoever, which is surprising, seeing as the creators at least took the time to give us clues as to who all of the mystery characters were in the beginning of the series. The events of Tamers is the only thing that keeps the moment from being a straight-up Ass Pull. And Mythology Gag aside, the appearance of the Savers and the claw-belt Agumon confirms that this universe shouldn't follow the same rules that Tamers does. So... Why?
- Sealed Evil in a Can: Chronomon. He would have been Sealed Good in a Can if not for Alphamon and Kain's involvement.
- Warm-Up Boss: The lead-up to Chronomon does this in stages. Armageddemon is fairly easy, but even a team which can win fairly easily could struggle against the four Pods. A team which can beat them with ease could well be slaughtered by the final boss itself.
- Well-Intentioned Extremist: Alphamon.