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Made of Iron: Jack Rakan, one of the names people have given him is "That damn guy you can stab with swords all you like and it won't do a thing, dammit"
Magic Contract Romance: Negi notes that there is a trend where Mages are known to marry their Minister/Ministra Magi.
Magical Incantation: Typically in unfamiliar languages, such as Latin, Greek, Sanskrit, and archaic Japanese.
Magically-Binding Contract: Pactio is the most obvious, but least straight, example. A straighter invocation occurs when Fate and Godel each try to make Negi sign one which would have the power of a geas.)
Magic Land: This would be the near-literal translation of Mundus Magicus.
Magic Missile: The functionality of the light-elemental Sagitta Magica attack spell is very similar to your standard Magic Missile. Other-element variations have more varied effects.
Magic Wand: The Thousand Master's staff works this way, as does the ring Eva gives Negi. Straighter examples appear when Yue and the rest of Ala Alba learn beginners' magic.
Make It Look Like a Struggle: Amnesiac Yue tells Negi to attack her when they accidentally meet, all the while wondering what exactly is she doing and why.
Masquerade: Mages are not supposed to reveal themselves to Muggles. Doing so puts them in danger of severe punishment, and Laser-Guided Amnesia for all involved if discovered.
Mass Teleportation: The portal to Mundus Magicus bears a strong resemblance to an airport.
Medium Awareness: The characters comment several times on the images that appear in the back of the panel to illustrate one of their thoughts or a flashback
Konoka hastily readies the Relax-O-Vision card used some chapters back when Rakan's taunting of the Amazon Brigade that's trapped them edges too close to Hentai for comfort.
During Misora's hilarious attempt to attempt to deny her identity through Blatant Lies, big glowing letters appear above her head proclaiming her name. She frantically tries to wave it away.
Misplaced Accent: In the English dub, Negi speaks like an American attempting the I Am Very British Received Pronunciation accent, not in anything like a Welsh accent.
Monster Mash: Negi's associates include a ghost, a vampire, a half-bird demon, and a dog demon. On the other side, the REALLY monstrous-looking bounty hunters are later seen casually relaxing in the same baths as Negi and company.
Negima!'s left-field ending; the gateport incident in Vol. 21.
A more minor one comes when Kurt Godel explains Negi's lineage and then gives Negi a We Can Rule Together offer. An otherwise serious moment is made funny with the inclusion of an RPG-style 'Yes/No' dialogue option.
Also thoroughly Lampshaded by Paru's drawings depicting all the different "Bad ends" that could happen at one point or another. such as Negi turning into an Ermine for allowing Magic to be exposed to the world.
Mundane Utility: Noticeable in Negima! and early in the manga. As the focus shifts to combat, these uses become less frequent and tend to be implied rather than shown.
For those people that can use them together (only three so far have been shown), it becomes a Yin-Yang Bomb.
My Kung Fu Is Stronger Than Yours: Not only do the major characters spend almost all their time off-screen either training or sleeping (and have been doing so for years), the training itself is a frequent plot point on-screen — especially if it's Training From Hell.
Naughty Tentacles: upon landing in Magicus Mundus, Chisame is attacked by a clothes-eating-octopus that seems to exist solely for putting in tentacle-rape-esque scenes
Not to mention Paio (of "Boobies!" fame), with sandworm familiars that used their tentacles to strip and almost sexually assault Nodoka.
Back in the Kyoto arc, Fate subdues Asuna by turning a bath into a bunch of watery hands that tickle her until she can't move. And this is after he accidentally destroys all her clothes.
Near Misses: stronger character vs. anyone using the time-warping bullets
Neck Lift: Negi's father does this to a demon in the flashback to the destruction of his village, and finishes it with a nice squeeze too.
Never Trust a Hair Tonic: A female variation, when short-haired Ako thinks she should grow her hair out to be more attractive. A (not so) helpful denizen of the magic world promptly gives her a magic hair-growth potion, which works perfectly for all of a minute before the hair begins to engulf her.
New Year, Same Class: Taken Up to Eleven. Negima's class doesn't change at all, despite there being around twenty other classes in the grade.
Hand-waved before it happened. It was stated that Mahora doesn't split up its classes.
Nice Job Breaking It, Herod: The attack on Negi's hometown was done by the Megalomesembrian Senate in a specific attempt to kill Toddler!Negi. It obviously failed, and now Negi knows, and boy is he pissed.
Ninja Pirate Robot Zombie: Would fit right in besides the Welsh ten-year-old kung-fu wizard school teacher who's also technically a prince who is the protagonist. Never mind Chao Lingshen, the time-traveling Magitek-wielding Martian mad-scientist restaurant owner who is fittingly the protagionist's decendant and totally wasn't BSing about that Mars thing either. And that's just to start.
Noodle Incident: There're actually quite a few. One including "Chizuru and a large number of spring onions", and another about Chisame's "First time on the net".
We also have Negi's "troubles" during Christmas and Valentine's Day.
Numerological Motif: Each member of the class their seat number takes great importance they are referred to by number at the start of the series and are on their Pactio Cards.
Negi's Pactio card number is 496 The Perfect Number of his 31 students. (As in he wouldn't be who he is without each of his students)
Luna's Pactio card number is 32 as in the newest student to the class
Rakan and Albireo's Pactio's with Nagi [2] numbers are both 1001
Evangeline herself is a blue-eyed vampire who is Really 700 Years Old. It was recently discovered that she herself is also a creation of the Lifemaker; exactly what kind has not been revealed yet.
Crops up again in the second Mou Hitotsu no SekaiOVD, the bit where Fate shatters stone!Asuna in Negi's dream. There's less Conspicuous CG, with better physics, in GaoGaiGar.
Offscreen Moment of Awesome: Seven years worth of moments with every member of class 3A's actions in the future and their work to help save Earth, Mars, defeat the Lifemaker and save Nagi.
And then there's Jack making shit puns before confronting Fate's minions during Godel's ball. He says he has to go take a dump, and then tells Fate that everyone has to wipe their own asses. Truly, the shithas hit thefan.
Old School Building: In the first anime this is the setting for the "kiss catch" game.
One-Hit Kill: Time-displacement bullets. (Interesting in that it's not a "kill" in the traditional sense, but tactically there's little difference.) Also, Code of the Lifemaker has this effect on natives of the Magical World.
Subverted later on; after Negi single-handedly wipes out a gang of bounty hunters, the leader starts muttering about revealing his true form. Negi gives him a mean look, and he goes back to cowering on the ground.
The Only One Allowed to Defeat You: In chapter 314, Fate is revealed to have survived, and is fighting Quintum to protect Negi's comrades. Because only he is allowed to defeat his rival.
On the Money: Buying out slaves = one martial arts tournament.
Actually an inversion: It makes perfect sense for a martial arts tournament to have a round million as a reward, but not so much for that to be the exact price of the slaves' debt.
Orwellian Retcon: How old is Negi, chronologically? Well, the initial magazine releases said he was born in the summer of 1993, making him about 9 years old in the prologue. The bound volumes changed this to simply "1994", consistent with his earlier admission that he's only 10 if you use kazoe, and Word of God reportedly has him at about eight and a half at the start of the series.