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In the US and Canada, the manga is licensed and published in English by Del Rey Manga. Publishers in other countries and languages include Tong Li Comics in Hong Kong, Chuang Yi in Singapore, Play Press Publishing in Italy, Pika Édition in France, Egmont Manga & Anime in Germany, Glénat in Spain, Editora JBC in Brazil, Tanoshimi in the UK, and Level Comics (PT. Elex Media Komputindo) part of Gramedia Group in Indonesia.
In Malaysia, the Malay version of the Negima books, named 'Magic Teacher! Ahli Magik Negi Magi', are retranslations of the Chinese edition. Evidence shows the names of the characters in Chinese style, such as Asuna as Shenlao Asuna and Konoka as Munai Xiang. Instead of printing "Ken Akamatsu" as the author, the name "Chesong Jian" is used – actually a Mandarin translation of Akamatsu's name in kanji. The characters' names were corrected in volume 15.
The manga is made up of several arcs:
- The Child Teacher Arc - After receiving his assignment, Negi becomes the English and homeroom teacher for Mahora Academy Class 2A. A general introduction section of the series, it mostly served as a basis for introducing the students and establishing the relationship between Negi and Asuna. Certain students gained particular development, including the Baka Rangers and the Sports girls, as well as individual focus on Konoka, Ayaka and Chisame. (Chapters 1-15, Volumes 1 & 2)
- Evangeline Arc - (Partner Saga as Akamatsu calls it)- After officially becoming the full year teacher for now Class 3A, Negi gains his first real challenge: battling against his student (and immortal vampiress) Evangeline A.K. McDowell and robotic partner Chachamaru Karakuri. The Pactio system is introduced in this section as well as Negi's ermine familiar Chamo, with development regarding Eva's relation with Negi's father, Nagi Springfield. To fight Eva alongside Negi, Asuna becomes his first partner. (Chapters 16-25, Volume 3)
- Kyoto Field Trip Arc - Following a lead, Negi takes the class on a trip to Kyoto to find more information on his father yet is forced to fight against Eastern mages with hired help. The arc focuses primarily on Konoka, both on her family's relationship to Negi's team as well as her own relationship with classmate Setsuna Sakurazaki. The arc also focuses on the blossoming feelings of Nodoka Miyazaki towards Negi and similar feelings beginning to emerge for her friend Yue. Nodoka, Setsuna, and Konoka become Negi's partners by the end of the arc. The end of the arc shows a drastic change in tone and atmosphere. The manga becomes more tense and action-filled. Suspense becomes a major issue, this arc symbolizing the turning point of the series (chapter 45 specifically). Mentions of a more sinister opponent are made through Fate Averruncus. (Chapters 26-53)
- Training/Wilhelm Arc - Seeing his own weakness after Kyoto, Negi begins to train with several students in order to become stronger. Meanwhile, an old evil from the past re-emerges at Mahora while tenacious rival Kotarou Inugami unexpectedly reappears and gains a new family. This arc begins to show the development of Negi's main team while Makie, Chizuru, and Natsumi all become involved in the events. Wilheim, like Fate Averruncus, is a pawn of a 'bigger and badder' fish that is yet to be mentioned. (Chapters 54-71)
- The School Festival (can be broken into sub-arcs) (Chapters 72-168)
- Pre-Festival: Mahora organizes a festival to celebrate the peaking power of the World Tree and 3A prepares in their own ways. Many characters are both introduced and put forward as the students prepare and one of them begins the first hints of a much bigger plan. Mentions are made of the World Tree's power. (Chapters 72-80)
- Festival Day 1: With the assistance of Chao's latest invention, the time machine Casseopeia, Negi partakes in many activities, including the class haunted house, patrolling with two students, dating three of them, and even helping one in a costume contest! He also takes parts in preliminaries for one of the big events of the festival: the Mahora Tournament. (Chapters 81-87)
- Mahora Budōkai: After making his way to the top sixteen, Negi fights his way through rivals familiar and unknown to reach the finals, including another member of the Crimson Wing. Meanwhile, Asuna slowly discovers more secrets from her past, and Chao begins to make her move, with guards, from Takamichi and Setsuna to Misora, after her. (Chapters 88-119)
- Festival Day 2: After the tournament, Negi takes part in more activities at the festival. Focused students in this section include Ako, who reveals her crush on an older Negi, the Library Club girls, and the bizarre friendship growing between Chisame and Chachamaru. Yue and Haruna become the fifth and sixth partners, respectively, by the end of this arc. (Chapters 120-131)
- Chao's Mission & Eight Days Later: With her plan finally in full force, Chao confronts Negi in combat with a surprise ending. Yet, troubles continue as an unexpected move throws Negi's allies into a world they never expected. (Chapters 132-144)
- The Battle of Mahora: After returning from their side-trip, Negi's team have a decisive confrontation against Chao, and Chisame finally relents into becoming Negi's seventh partner. (Chapters 145-162)
- Post-Festival: With the festival finally over, Negi comes to a decision regarding his search for his father and his relationship with Asuna. Slight focus is further made regarding Misora and Sports girls Yuna and Akira. (Chapters 163-168)
- Journey to the Magic World (can be broken into various sub-arcs) (Chapters 169-335)
- Preparations: Negi and his partners form their own brigade, the Ala Alba (White Wing), and prepare to travel to the magic world to try to find information about Nagi. They are joined by Negi's childhood friend Anya and accidentally by Yuna, Ako, Akira, Makie, and Natsumi, who unknowingly followed after. (Chapters 169-185)
- Separation: As they arrive, they are ambushed by a group of mages led by Fate Averruncus. The gate is destroyed and Negi and his group are defeated and scattered across the Magic World. Himself framed for the attack on the gateport, and discovering that Natsumi, Akira, and Ako were forced to sell themselves into slavery to pay for treatments when Ako suddenly took ill, Negi enters a fighting tournament under his father's name to raise the money needed to pay off their debt, at the same time alerting the others of his whereabouts, so that they all can meet up at the lost city of Ostia. (Chapters 186-200)
- Reunion: Negi begins training under Rakan, a former ally of Nagi and member of Ala Rubra. In order to obtain the power to defeat Fate, Negi decides to abandon the path of his father and chooses to specialize in Dark Magic, just like Evangeline. Kazumi becomes Negi's eighth partner. Meanwhile, Negi's lost companions start to learn the ropes of their new environment and are gradually reuniting with him at Ostia. (Chapters 201-220)
- The Ostia Festival
- Ostia Festival - Part 1: The festival celebrating the end of the war that devastated the Magic Realm 20 years prior begins. Fate Averruncus confronts Negi asking him not to interfere with his and his associates' plans in exchange for a safe passage home for Negi and his students. At Asuna's behest, Negi declines Fate's offer resulting in a vicious battle between the two parties until the arrival of Rakan forces Fate to retreat. Little they know is that the real Asuna was captured during the battle and held captive alongside Anya by Fate, while a body double takes her place. After Rakan tells the story of Ala Rubra to the group, Kaede becomes Negi's ninth partner. (Chapters 221-234)
- Ostia Festival - Part 2: Negi and Kotarō qualify themselves for the festival's fighting tournament, but their hopes to win the first prize are crushed when they find that Rakan himself is also participating. However, the duo refuses to give up and enters on a heavy training routine under the supervision of Evangeline and some old friends of Ala Rubra, including Princess Theodora of the Hellas Empire, who forms a pactio with Negi, making him her partner. (Chapters 236-239)
- Ostia Festival - Part 3: Negi and Kotarou complete their training and confront Rakan in the final match of the tournament. Negi and Rakan fight to a standstill, with Negi pulling out a number of new deadly techniques after almost being defeated numerous times, while Rakan recognizes him as a "man". (Chapters 240-248)
- Post-Festival: With Rakan's help, Negi manages to gather enough money to release Ako, Akira, and Natsumi, who were made into slaves, and his party's following objective is to reunite with their remaining missing members and return to their homeworld together. While Negi and Nodoka finally find Yue, Setsuna becomes Konoka's partner. Negi also meets Kurt Gödel, the Governor of Ostia and a former member of Ala Rubra who reveals Negi's hidden heritage as well as the identity of his mother. (Chapters 249-255)
- The Governor's Ball: Kurt Gödel invites Negi and his friends to a ball offered by the Ostia Government. He also promises to lift the bounties on their heads and reveal to Negi the truth about his parents if he agrees to attend. The gang discovers that Mundus Magicus is a parallel dimension version of Mars. Jack Rakan engages Fate Averruncus and his Ministrae in combat. Meanwhile, Ku Fei and Chachamaru become Negi's tenth and eleventh partners, while Koutarou decides to become a Magister too having Natsumi as his partner. (Chapters 256-264)
- Recollections: Gödel reveals to Negi the story of his parents including how his mother was unjustly tried and sentenced to death by the Megalosembrian Senate, and saved by Nagi at the brink of her execution. However, when Gödel asks Negi to join him against the senate, Negi figures that he is not being honest at all (his objective being rescuing only the human population of Megalomesembria) and refuses his proposal. Cornered by the Megalosembrian army, the members of Ala Alba are forced to fight their way out. (Chapters 264-274)
- Return of Cosmo Entelecheia: Ala Alba's battle against the Megalosembrian army is interrupted by the sudden appearance of Fate's organization, the Cosmo Entelecheia, whose forces easily crush all opposition. Meanwhile, Nodoka discovers the ultimate secret of the Magical World, as just like the world itself, the majority of its inhabitants are created by magic, including Rakan and the friends the girls made during their travels who are effortlessly erased by Fate and his army. However, Nodoka manages to use her powers to read the mind of one of Cosmo Entelecheia's leaders, and discovers a way to bring them back. (Chapters 274-282)
- Asuna's Location: Being alerted by Rakan's last words, Negi manages to uncover the true identity of the fake Asuna by forming a pactio with her. She happens to be Shiori, a member of Cosmo Entelecheia who decides to join forces with Negi and reveal the location of the real Asuna, becoming his twelfth partner. Meanwhile, Asuna hears from Fate the true objective of his group; to erase the magically created inhabitants of Mundus Magicus and transfer the rest of its population to Earth before it eventually collapses and Negi begin to train with Evangeline, Setsuna, and Kaede to suppress Magia Erebea darkness. Meanwhile Negi formed his thirteeth to fifteenth pactio with Ako, Yuna, Makie after training to suppress the Magia Erebea darkness. (Chapters 283-290)
Negima! was involved in a controversy surrounding the censorship of the English-translated manga in North America, typical of Akamatsu's penchant for fanservice and risqué humor. Fans fell upon initial rumors of potential edits by Del Rey, and upon receiving news of this, immediately began fighting against the changes. The compromise reached was to release the book uncensored but shrink-wrapped, which some collectors feel can cause damage to the books. Since Volume 14, the books have been released without the shrink-wrap.
Del Rey's releases contain fully translated versions of the omake(s) found in the Japanese versions (which include character sketches, fan art, and information about spells and related concepts), as well as various notes about Japanese culture and other things of interest not found in the original omake(s).