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Yuuichi Tate is an Ordinary High School Student transferring in to the new school of Fuuka Gakuen. As he rushes to avoid being late for his first day at the new school, he comes upon the sight of two girls battling each other - and using decidedly supernatural powers to do so. As he stands there gawking in amazement, one of them notices him and demands to know what he is doing there - shortly before her close proximity to him creates a reaction of some sort that leaves them both stunned.

And thus Yuuichi ends up getting roped into the world of the HiMEs, girls with the ability to wield magical weapons called 'Elements', and with their 'Key' present, the ability to summon giant beasts known as 'CHILD'. These are used in their battles to protect the school (and by extension the rest of the world) from monstrous creatures known as 'Orphan's. As the 'Key' to the two dueling girls, Mai Tokiha and Natsuki Kuga, his life has just become a whole lot more complicated.

The manga version of Mai-HiME was conceived as an Alternate Continuity to the anime counterpart, with most of the characters having noticeably different backgrounds and personalities. While it has never managed to achieve the popularity of its anime counterpart, it nevertheless has a cult following. The series is available in paperback in North America, licensed by Tokyo Pop.

The manga shares a majority of tropes with the anime. Here are several that stand out within the manga itself:

  • Anti-Magic: Near the Gateway, it is impossible to summon Elements or Childs.
  • Asshole Victim: The first (and in this version, only) person to demonstrate what happens when a Child is destroyed is the teenager who tried to sexually assault Shiho and was responsible for injuring Yuuichi's arm).
  • Badass Normal: As de facto main character, Yuuichi is noticeably more action-y than his anime counterpart, despite not having any powers aside from kendo training to stand on. The fact that he's needed for the two female leads to activate their latent abilities doesn't hurt either.
  • Berserker Tears: Mai in the final arc.
  • Beware the Nice Ones: The Obsidian Lord, Big Bad of the whole story? Takumi Tokiha, Mai's sickly younger brother.
  • Brought Down to Normal: Shizuru Fujino is not a HiME in the manga, whereas Haruka Suzushiro, who was a borderline Badass Normal in the anime, is a HiME in this continuity. Their importance to the story has also been switched.
  • Calling Your Attacks: Used to a much greater extent in the manga.
  • Clothing Damage: The first fight against an Orphan in the manga has one of the female lead's school jacket being torn open. It goes downhill from there.
  • Combat Commentator: Chie and Aoi, during Haruka and Yukino's challenge of the main Power Trio.
  • A Day in the Limelight: A few of the supporting characters (such as Mikoto and Akane) are given their own eponymous chapters that reveal a little bit of their backstories.
  • Disney Death: Takumi appears to die, only to become the Obsidian Lord. Haruka, Yukino and Midori are seemingly killed in the climax, but survive.
  • Don't You Dare Pity Me!: Mai in the Manga hates being thought of as dependent or pitiable.
    • Natsuki punches Yuuichi when she thinks he's helping her out of pity, after a Hannibal Lecture by her mother asking her if she wants to be helped by someone motivated by pity.
  • Fan Service: See entry on 'Clothing Damage'.
  • First Girl Wins: Upon his arrival to Fuuka, Yuuichi brushes past a crying Mai. They end up kissing in chapter 22, and the Mai-Otome manga reveals that they became husband and wife.
  • Get a Hold of Yourself, Man!: Done by Natsuki to Mai in the final arc. Also attempted by Yuuichi against Shiho, but that one doesn't work.
  • Honor Before Reason: It gets pointed out several times to Yuuichi that he's really more of a liability on the battlefield than anything else. Doesn't stop him from heading out anyways. (And as mentioned above, Mai and Natsuki kinda need him there, as unlike in the anime, the Key must actually be present and fairly close for the HiME to summon her child)
  • Hot Springs Episode: Surprisingly, a brief interlude when the HiME are trapped in an underground cavern.
  • Lighter and Softer: The characters' emotional trauma is less severe than in the anime, and instead of fighting each other, they end up fighting increasingly dangerous common enemies.
  • Love Triangle: Mai and Natsuki over Yuuichi. Shiho later becomes a third contender.
  • The Masquerade: Completely averted in the manga - the characters fight in open daylight, are not Invisible to Normals, and usually have to deal with the consequences of their overly-destructive actions.
  • No Ontological Inertia: Inverted - if a 'Child' (the created being) dies, the 'Key' (one half of the creator) goes with it.
  • Not Brainwashed: Mai pulls this trope during a brief Face Heel Turn in the manga's final arc.
  • Not Quite Dead: Natsuki's mother, who surfaces as a villain after Nagi's initial defeat, but ends up doing a Heel Face Turn toward the end.
  • Refuge in Audacity: A lot of the things that happen in the manga are quite over-the-top, especially near the beginning.
  • Shock and Awe: Haruka's powers and Child have lightning-based powers.
  • Shoot the Dog: Akira plans on killing Takumi before he can become the Obsidian Lord, but is too late and fails.
  • Shut UP, Hannibal: Delivered by Yuuichi to the Big Bad, dismissing his Motive Rant by saying that he shouldn't make his sister cry.
  • Sorting Algorithm of Evil: Single orphans -> the rival Ori-HiME unit -> Nagi -> Searrs -> The Obsidian Lord.
  • Trauma Conga Line: It wasn't enough for Mai to learn that she'd been putting Yuuichi in mortal danger since the first day she met him. It wasn't enough for her to have to fight her Brainwashed and Crazy best friend. It wasn't enough for her to witness her love interest get beaten within an inch of his life by his childhood friend. It wasn't even enough that her younger brother died. The final straw was when her brother ended up being reborn as the Obsidian Lord, sending Mai straight into a Heroic BSOD.
  • Vitriolic Best Buds: Natsuki and Mai eventually become this; their arguments are more heated than in the anime, and they are rivals over Yuuichi, but they care for each other.
  • With Great Power Comes Great Insanity: Overusing Princess Earrings results in the user being susceptible to brainwashing by the Hime Star.
  • Your Princess Is in Another Castle: The victory parade after Nagi's defeat is spoiled by Searrs' arrival and hostile takeover of the school.
    • The Searrs have barely been defeated when the Great Cosmo Beauties appears and Takumi seemingly dies, only to be reborn as the Obsidian Lord.