Gecko Ending: A mild example: the anime ends with Homura walking towards a Bolivian Army Ending while manifesting a pair of Lovecraftian butterfly-like wings, which the game dubs the Black Wings of Corrosion. The manga ends on a far more bittersweet note with Madokami taking her into the afterlife.
Genre Deconstruction: In Real Life, a Magical Girl is a soldier fighting in an urban environment without infrastructure supporting her and whose enemies may or may not be innocent looking civilians. The magical animal friend is deliberately giving these powers to children who may not have the emotional strength and experience to handle them.
Ghost in the Machine: What happens during a contract is that Kyubey takes the 'little girl inside the head' (i.e. soul) out of his contractee and turns it into a soul gem. Thus, a magical girl's body is a magical meat-puppet controlled and powered by this gem.
Meganekko!Homura does a very shaky, unsure version of this, but it's possibly justified by the fact that It's before her power-leveling, and she's still recovering from that heart condition.
The Glasses Come Off: Just before the last "iteration" of past, Homura takes off her glasses and uses her powers to restore her eyesight. This marks the transition between "Moemura" and the Homura that is introduced in Episode 1.
Zigzagged when Charlotte eats Mami in Episode 3 we don't see the bite but afterwards we see it dive down and tear the corpse apart like a wild animal. It pans away again, to the disbelieving and horrified Sayaka and Madoka watching on, but the sounds continue—this just makes it worse.
Averted in the manga, where we get to see the entirety of Mami's demise.
Gratuitous French: The themed cafe that will appear in Matsudo, Chiba is called Cafe du Madoka Magica (Cafe of the Madoka Magica). "Du" (de + le) is masculine; it should be Cafe de la Madoka Magica.
The language of choice for the bizarre creatures at the end of the first episode. They speak in a highly disturbing, screechy and childlike voice, which is even scarier if you can understand bits of what they're saying. Those flying scissors aren't just for show... note For those who really want to know...: They're saying that they've never seen flowers like them before. This would be creepy enough as it is, but then they say things like "Let's just cut them off." and "We present the roses to our queen."
In Episode 2, there is some German scribbled on the wall. It is a quote from Faust about a destroyed world being rebuilt...
Grey and Gray Morality: Madoka is the only 100% good character. Everyone else in this series has a little good and bad in them. Even Kyubey has an understandable reason for what he does, and the witches are fallen heroines.
Grilling the Newbie: The girls in Homura's new class grill her about her past, which she replies with as dispassionate 'I was hospitalized for a long time' as humanly possible. Because she has experienced this routine countless times.
"Groundhog Day" Loop, Save Scumming: Homura's wish was to 'start over her relationship with Madoka' and 'protect her instead of her protecting me'. Thus she gained power over time and can reset the month between Madoka's debut as a Magical Girl and her death/corruption because of Walpurgisnacht. As for Save Scumming, her repeated resets are comparable to a player attempting to save a certain NPC by resetting after every failure and trying a different strategy next time, picking up out-of-character knowledge of the enemies and events of that chapter in the process.
The Greatest Story Never Told: In the end, Homura is the only living witness to everything that has happened, and the new version of Kyubey says he'll have to take her word for it since no proof of it remains.
Guest Strip: PMMM continues the trend of inviting talented semi-pro and Pixiv artists to draw eye catches and end-of-episode preview art, something that has been traditionally done at the last few pages of Doujinshi for decades. The full list of ending cards can be found on the trivia page.
One of Homura's abilities. It's shown that she's got an entire armory hidden literally up her sleeve.
Mami has the ability to summon muskets from under her hat and skirt.
Sayaka once summons swords from her cape.
It's not entirely apparent where Kyoko stores her spear because it sometimes vanishes between shots with no evidence of her dispersing it (Episode 8).
Hard Work Hardly Works: Like most things in this show, ruthlessly played for drama. No matter how hard or how many times Homura tries, she can never overcome Madoka's destiny because her effort is exponentially making Madoka's magical potential (and thus her desirability to Kyubey) stronger. Likewise, Walpurgis is utterly unaffected by her attacks, possibly for the same reason; Madoka is the only one with the chops to challenge her, no matter what Homura does.
Sayaka is the only one to use a sword as her weapon. Although her outlook and motivations fit the classic hero mold, she is far and away the weakest of the magical girls and eventually turns into a witch.
Homura steals a katana from the Yakuza but she's an anti-hero and she never uses it.
Kyoko kills Oktavia (aka Sayaka) with an explosion that kills her as well so the latter won't die lonely.
If what Kyubey told Madoka in Episode 9 is true, becoming a magical girl can be viewed as such, with delayed consequences. A magical girl's sacrifice extends the life of the universe.
In another timeline, after both of them suffered mortal wounds from failing to defeat Walpurgisnacht, Madoka brightens Homura's soul gem with her only remaining grief seed, thus giving the latter the chance to go back again and try to save everyone but at the cost of dooming her self to become a witch. Cue the request for and subsequent Mercy Kill.
Madoka pulls this again in the end by using her wish as a Reset Button that prevents witches from being born (and gives the already witchified magical girls peaceful send-offs) ... but while doing so, erases herself from physical existence because she has risen above physical existence. Bonus, the finale aired on Good Friday. Significant? With her last words to Kyubey ordering him to fulfill her wish, it's made clear that she doesn't care what she becomes as long as the world is saved.
Kyoko in The Different Story uses Oktavia's Grief Seed to cleanse Mami's Soul Gem, but doesn't have another one left to use on herself and runs out of magical energy before she has a chance to cleanse her Soul Gem.
It was shown in Episode 10 that in the first timeline, Madoka sacrificed herself to defeat Walpurgisnacht. This is Homura' reason to make a contract with Kyubey.
He Who Fights Monsters: Witches are magical girls who let their soul gems become too corrupted. Sayaka is a more specific example.
Hive Mind: Kyubey, according to an interview with Urobuchi.
There are many bodies, but only one consciousness. Therefore, even if you kill the body, there isn't any sort of damage. Killing one is just like pulling out a single strand of hair. The scene where Kyubey eats his corpse was a scene that came in after the early stages of the script; I was trying to write Kyubey as something that humans can't relate to. Imagine what your response would be if one of your compatriots had just died.
In-universe example in Episode 9. The main characters ask Kyubey if it's possible to restore Sayaka to human form. He replies that it's never been done before. Not only does it fail, but he was counting on it failing and only presented the hope as a trap.
It could be argued that the anime timeline — as opposed to the timeline in the epilogue / the previous timelines is a Hope Spot. Everything seems to be going well from Homura's perspective: Madoka hasn't contracted and that's all that matters. Then it turns out that even with enough military hardware to be a One-Man Army she can't stop Walpurgisnacht, Kyubey knows about her time traveling, she's the cause of all Madoka's problems in the newer timelines, and her resets are making things worse. It takes the events of Episode 12 to pull everything out of the tailspin.
Honor Before Reason: Sayaka refuses help from any magical girl who does not meet her ideal of justice. She gives Kyoko a grief seed from a witch just because Kyoko briefly helped her in the fight. She also refuses a grief seed from Homura despite knowing that her soul gem was too tainted for her to go on that way.
Sayaka attempts to be The Cape and eventually breaks down.
Kyoko ceased being a hero at all (until Episode 9).
Homura has watched her dearest friend die or witch out; in one time line she had to Mercy Kill this friend.
Hyperspace Arsenal: Many magical girls can generate a multitude of weapons to fight witches. Homura has a literal one of these; she stole rocket launchers from the Yakuza and the Defense Force and pulls them all out when needed.
I Just Want to Be Special: Madoka starts off like this. When the call of 'one wish in exchange for service in battling monsters' comes, she admits to not being interested in the wish as much as helping others in a cool outfit - in her own estimation, she's not especially smart or talented, and she wants to accomplish things. It doesn't last. Homura tries to disabuse her of the notion at one point, saying that even if she isn't unique, she's still loved and needed by others, and shouldn't think of herself as useless.
Mami mostly sticks to summoning enchanted muskets, but can enchant a bat to harm familiars and can create a barrier using a length of chain as a boundary and conduit.
Kyoko creates a pair of binoculars so she could spy on Sayaka.
Homura once used her powers to fix her eyesight despite the fact that her power has nothing to do with healing. This one could double as fridge brilliance when you think Homura could be using her powers to time-travel her eyes back to a time when she didn't have bad eyesight.
Kyubey has a variant of Resurrective Immortality. Homura pumped one of his bodies full of lead and one second later an identical Kyubey jumped out of nowhere and ate it. He claims to have an endless supply of bodies.
In The Stinger of the anime. Homura might be proving that you can theoretically live forever as a magical girl as long as you don't exhaust your magic and never give up hope. The manga goes a bit further in the timeline by showing that eventually Homura stops fighting and joins Madoka beyond existence. It is not shown when or how this happens.
At the end of the anime, Madoka gains Complete Immortality becomes she's now an abstract concept/goddess.
In Medias Res: Playing with a Trope. Episode 10 explains the alternate timelines, but every timeline has technically the same start, due to being parallels of each other. However, the start for the anime is explained in Episode 10, which explains Homura's intentions that were not explained in the first two episodes. In other words, the anime starts at the how many times is it now parallel timeline, but we learn of the beginning in Episode 10.
Homura has used her power to reset time to approach the series a countless number of ways, but the outcome is always Madoka becoming a magical girl and either dying or turning into a witch.
When Madoka makes her final wish, despite having radically changed the course of human history (namely, those killed by witches no longer died that way), Mitakihara still exists more-or-less the same, along with every character other than Madoka herself.
Sayaka always becomes a witch, and always does so at the exact same train station (post-Godoka, she disappears there instead).
Madoka's mother tells her to make mistakes when she's young, because the older you get, and the more responsibilities you have, the more important it is to not make mistakes, and recover quickly when you do. When Madoka observes that it'll hurt, her mother tells her adults are always in pain, and that's why adults can drink alcohol: when you're an adult, it's only as fun as it hurts! Later on, we find out that Kyubey's contract demands that Magical Girls experience despair equal to the happiness gained by their wishes, and, drawing from most magical girl show tropes, it ties in Madoka's mother's words to a coming-of-age theme.
In the hospital Kyosuke says he can't feel the pain anymore after smashing the CD Sayaka gave him in a fit of rage. After Sayaka becomes Ax-Crazy and Laughing Mad in her fight with Elsa Maria she repeats this.
One of Kyubey's sales pitches to Madoka is that she can wish herself to become a god if she so desires because of her enormous magical potential. In Episode 12, Madoka's wish breaks the laws of causality, prompting Kyubey to ask if Madoka really wishes to become a god. Madoka simply states that he can call her whatever he wants, so long as her wish is fulfilled.
It Always Rains at Funerals: When Sayaka's body is recovered and she is given a proper funeral in Episode 11, it immediately starts raining.
The witch Charlotte starts off looking like an adorable little stuffed doll.
Kyubey himself is far more dangerous than he appears.
Knight in Sour Armor: Madoka and Homura both exemplify this, but especially Madoka. She sacrifices all semblance of her own identity to change the magical girl system. She creates a new world where suffering runs just as rampant as ever, acknowledging good cannot exist without evil. And why? Because, by god, magical girls deserve to die happily, and she's willing to become the embodiment of hope itself in a despair-filled world.
This trope was one reason why the storyline was predicted ahead of time, due to the numerous Faust references. Lists are on The Wiki Rule (here), the Trivia page, and the Fridge page. There is, however, one notable one that is very easy to pass off: Homura, near the end of the anime, is shown with only one of Madoka's hair ribbons. Madoka gave Homura both. It may be justified in that she keeps the other one somewhere safe, and is why she's willing to give Madoka's mother the other one.
In the manga, Homura wears her hair in pigtails in the new universe by using both ribbons.
Leonine Contract: In at least one case, Kyubey has forced a wish out of someone because they have no other options. Mami, for instance, says she didn't have a choice because she was dying from a car crash.
Level Ate: Charlotte's labyrinth is this while also having a hospital theme.
Lighter and Softer: The second drama CD (appropriately named "Sunny Day Life") is probably the closest we will get to a canon depiction of the show as a conventionally cute Magical Girl series.
Limited Wardrobe: Almost every girl is shown with two outfits each: her school uniform (Homura, Sayaka, Mami)/one casual outfit (Kyoko) and her magical girl costume. Madoka is slightly better; in her PJs on occasion as well as when Ultimate Madoka is seen with a more complex uniform. The manga avoids this.
Love Makes You Evil: Played with in regards to Sayaka. Since she became a Magical Girl in order to heal Kyosuke, it fills out one of the main aspects of the trope. Kyoko later suggests she go a step farther and add a dose of If I Can't Have You by breaking his arms and legs so Sayaka can be the only one he can depend on. Once Hitomi tells Sayaka she has her own feelings for Kyosuke and says she intends to act on them, it essentially leads to Sayaka's My God, What Have I Done? moment, which then leads to her Despair Event Horizon /witch transformation.
Love Triangle: Hitomi reveals to Sayaka that she also likes Kyosuke and plans on confessing to him. She gives Sayaka 24 hours to do something about it ... and since she doesn't, she acts on her own word and confesses. See also the above trope.
Made of Evil: The Witches are born from despair and curses. It is their very nature to kill people.
Made of Iron: Justified. Magical girls have their souls separated from their bodies which allows them to take hits that would severely injure or kill any normal human being. Any damage can be repaired by magic later as long as the soul gem stays safe.
Magical Girl: It's half of the title but it could also be called young witch.
Magical Girl Warrior: The job of a Magical Girl is to hunt and slay witches. There are archers, gunners, swordswoman, etc.
Magic Skirt: Madoka's magical girl skirt is justified since there are a lot of frills underneath. The other skirts are rather short and the show has a tendency to show a lot of leg, but never more. This especially apparent when Kyoko is carrying Sayaka in her arms in Episode 9. There is a side shot with Sayaka's leg conveniently in the way.
Make a Wish: Everyone who wants to become a magical girl is granted one wish and each magical girl will gain different abilities depending on the nature of her wish. It sounds great until the characters learn that each wish has a price which will get higher with each person that will be affected by it.
Manipulative Bastard: Kyubey's MO is to appear to MG candidates when they are emotionally vulnerable and thereby unable to refuse a Miracle Contract.
In Mami's backstory he appeared when she was dying from a car crash.
In Kyoko's backstory she was homeless and starving.
In Episode 9 he convinces Kyoko to try (and fail) to save Sayaka as it would lead to her death and force Homura to fight Walpurgisnacht by herself, thus requiring Madoka to become a magical girl.
Mask of Sanity: Mami's actions at the end of the third timeline make it clear that she's wearing a very easily broken one of these. It's significant enough that Homura even outright discusses it during Rebellion.
Maybe Magic, Maybe Mundane: Homura's apartment is a bit of a mystery. It's a White Void Room full of floating video screens that can display images directly from Homura's memories. It seems like it must be magical, since the rest of the world is only marginally more high-tech than ours and she must be recreating the whole thing after every time reset. But Homura has very specialized powers that don't really lend themselves to building a hyper-futuristic room.
There is a good reason they are called magical girls. It's Japanese wordplay: In written Japanese "magical girl" contains the characters for "young girl" and "witch" — "magical girl" can then be read as "young witch".
Kyubey's full name is Incubator, which hints at his actual purpose—and coincidentally is formed from the same root as incubus.
The name Madoka can be written with the character for "circle" or "round" in Japanese reflecting the cyclical nature of the magical girl-witch incubator relationship as well as the circular repetition of timelines that revolve around her. It could also be written with the character for "wish" or "ambition"; the connotations of that should be obvious. Her last name, Kaname, can also be read as "pivot" or "vital point", which is apt to say the least due to Homura's time-meddling making Madoka's existence the pivotal point of every timeline she creates.
The final and most powerful witch seen in the series is Walpurgisnacht. This is the name of spring festival in Central and Northern Europe, and tradition dictates that it is a time that witches would gather together. Walpurgisnacht is a fusion of many different witches.
"Sayaka" can mean "bright" or "fresh". "Miki" could be written as "tree trunk" or as "sake offered to the gods". Trees are generally associated with witches in the series, especially Walpurgisnacht, and an offering to the gods is a sacrifice. So Sayaka Miki is a "fresh sacrifice" whose very name foreshadows her becoming a witch.
Sayaka receives one from Kyoko because she has become a witch.
Madoka asks this of Homura in one timeline because she doesn't want to become a witch.
At the end of the anime, Madoka performs a Cosmic Retcon that basically does this to every magical girl that is about to become a witch (including ones that existed in the past) by taking them someplace else.
Metaphorically True: Kyubey's multiple truth statements can be easily misread by those not adept at picking out logical fallacies. When asked if there is any way to turn a witch back into a magical girl he says, "That's impossible" followed by "Magical girls do impossible things all the time". An emotionally distraught fourteen year old isn't likely to realize that these two statements are unrelated (just because you can do some impossible things does not mean you can do all impossible things) until it is far too late.
Million-to-One Chance: What Kyubey says about Kyoko's desperation move — it's never been tried, it's completely illogical, and even he doesn't think it'll work — raises all the flags for this trope. It doesn't work. It's completely illogical, so of course it doesn't work.
A Million Is a Statistic: Kyubeys have energy quotas per planet. As long as they fulfill their quotas, they don't care if a whole civilization, along with their planet, perishes.
This happens to Madoka, when she was caught in the witch Kirsten's barrier. The witch then uses her powers to torture Madoka by re-playing Mami's death over and over while subjecting her to Body Horror.
Kyubey does this when he shows Madoka how the world has been affected by his contracts, and how if it wasn't for the Incubators humanity would still be in caves.
In one scene, Mami achieves this trope using only an unlikely number of single-shot rifles.
Episode 10 shows Homura discovering this. Nothing says 'magical girl' like a squad automatic weapon.
In Episode 11 when Homura attempts to take on Walpurgisnacht alone, there is a long one-sided battle consisting of Homura expending a small army's worth of weaponry against Walpurgisnacht, including rockets, mortars, and a naval barrage. Unfortunately, it's nothing but The Worf Barrage.
More Hero Than Thou: Every magical girl or magical girl candidate is adamant about being the only one who will have to throw herself on the blade for the sake of somebody else. As they all get in each other's way doing this, it causes an amount of conflict that would be downright ridiculous if it weren't so depressing.
Mami is seen as the exception by Sayaka, Madoka, and even Kyubey, as she was willing to go out of her way to save them and show them the ropes before they decide to become magical girls, and has been hunting down witches to protect people.
Lose to Walpurgis alone and see it destroy the city (possibly killing Madoka), or
Defeat Walpurgis alongside Madoka and see Madoka eventually destroy the world, or
Rewind time again, thus making Madoka (and the witch she eventually becomes) more powerful and able to destroy even more.
On top of all that, if she accepts that her situation is hopeless, the despair will turn her into a witch as well.
The Movie: Three - a two-part compilation followed by an entirely new story picking up where we left off.
Mundane Made Awesome: In Episode 7, after having her advice rejected by Sayaka, Kyoko is shown furiously taking bites out of an apple.
Mundane Wish: In Episode 3, Madoka can't decide on a magical wish but wants to help Mami in her fight. Mami suggests that she use her wish to ask Kyubey for a cake feast to celebrate their partnership.
Murder-Suicide: In one of the alternate timelines, Mami snaps when she finds out that magical girls eventually become witches. She succeeds in killing Kyoko, but is killed by Madoka before she could kill Homura.
Musicalis Interruptus: In Episode 8, Kyubey finally manage to convince Madoka to make her wish while the overly optimistic music is building up in the background. However, Homura puts a stop to not only the proceedings, but the music as well.
Kyoko felt this way due to her telling Sayaka her backstory, and why she's such a Jerk Ass who only cared about herself. It helps explain why Sayaka began to care less and less about the reason why she became a magical girl in the first place. As well as finding out more about their roles and the gems. This may be one reason why she seemed to be trying so hard to help Madoka save her later on.
Mythical Motifs: When Kyoko and Madoka discuss the mission to confront the witch Oktavia (aka Sayaka), a pair of windchimes can be seen in silhouette: a diving mermaid and a unicorn rallying itself to charge. Oktavia's motif is the mermaid. The unicorn is likely to represent Kyoko, who wants to "purify" the witch (as unicorns did water). She is ultimately forced to kill her using her spear, hence the unicorn rearing up and lowering its horn for the attack. It's also revealed in the PSP game that Kyoko's witch form rides a unicorn.