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A plothole is a gap in a storyline that goes against the flow of logic established by the story's plot. While there are very few true plotholes in the .hack universe for which no possible explanation exists, this page lists the major unexplained and unexpected inconsistencies in the .hack world.
Midori fighting Haseo
The fight between Haseo and Midori has different outcomes in (book) .hack//cell where Midori actually lost her 'victim' fight against Haseo; whereas Haseo lost a battle to Midori in (anime) .hack//roots.
Also, in the anime, she is seen using her broadsword Dragonblosom in order to block some of Haseo's attacks, though in the book she does not even have the weapon out to show, and Haseo makes a comment that is probably the first and last time he will fight an unarmed opponent.
The First Fight Between Azure Kite and Haseo
In Rebirth, Haseo is seen fighting against Azure Kite. During the fight Haseo uses every skill in his arsenal, including all three of his weapons. However Azure Kite merely stands still and deflects everything Haseo throws at him, going so far as to delete his Scythe before data draining him. However, Roots depicts a different version of the fight, with Azure Kite using super fast movement and flight to dodge Haseo's attacks before data draining him. Both Rebirth and Roots are canon, however their depictions of this fight are vastly different.
This is probably due to artistic differences between the anime and the game. This aesthetic inconsistency between the games and anime is actually quite common for many effects (such as the warping ability used by the Phases), but due to the very limited overlap of specific scenes, this is usually not a problem. As both versions of this scene have the same outcome, there is no real effect on the integrity of the story.
During the G.U. Games, Haseo has a couple flashbacks to events occurring during the first half of Roots. Although Shino was wearing her pink color scheme at the time, this appears as her later black costume throughout the flashbacks. Also in Roots Shino retains her pink hair after switching costumes, while in G.U. her hair is silver.
This could be symbolism of something in Haseo's mind, though it is also likely that it is just another one of the many aesthetic differences between the games and the anime. The hair difference in particular seems to be a style difference.
Although an important aspect of video games would be a character's level, they are not as important within the .hack series. For example, a level 133 Haseo was defeated by Azure Kite in Rebirth, but Haseo later defeats Azure Kite at level 50 with the help of party members. Even though Haseo was at a lower level, it was used to represent how Haseo couldn't do everything on his own, and how he needed friends to accomplish his goals. In addition, Tabby obtains the weapons Feline's Soul as a newbie and immediately equips them, but when she joins Haseo's party in Redemption, the weapons are level 116. Obviously she wouldn't have been able to equip level 116 weapons as a newbie, so character levels aren't really important within the .hack series, as exemplified by the many contradictions within character levels.