The movie begins with a sequence where Homura narrates about the existence of magical girls while her soul gem floats through an open window and into an underwater-esque void.
The setting changes to Mitakihara City. A new kind of monster called a "nightmare" appears near a movie theater, which alters reality. The nightmare attacks the city, but is then confronted by Madoka, Sayaka, and Kyoko. The nightmare escapes into a dining room. Mami can briefly be seen in the background with a strange creature that resembles the witch Charlotte on her shoulder. Music begins playing as Madoka, Sayaka and Kyoko arrive carrying food, which they feed to the nightmare. Finally Mami walks up to the nightmare. The creature on her shoulder, who is later shown to be called "Bebe", slides down on the table carrying a cup of tea. Time suddenly stops for the nightmare. A flash of light comes from Bebe's teacup, bathing the room in light. The magical girls smile.
Suddenly Madoka wakes up in her room, like she did after the dream in episode 1 of the anime. She greets Kyubey, who is also sleeping in her room. Kyubey appears to be incapable of human communication and acts like an animal. What follows is a recreation of a sequence from the anime's first episode. Madoka greets her father while he's cutting tomatoes and forcefully wakes up her mother. In the washroom, there is a divergence from the anime when Madoka reveals that Hitomi and Kyosuke are going out. However, she claims they're having some relationship difficulties. Madoka also says that Kazuko is suddenly talking about the end of the world, which Junko blames on her relationship problems. Finally, Madoka says a transfer student is coming to their class. Notably, Madoka is wearing a magical girl ring, and Kyubey is also in the washroom soaking himself (as in episode 2). We then see a repeat of Junko catching Tatsuya's dropped tomato and then bidding her family goodbye as she leaves for work. Madoka then hurries off to school with a piece of toast in her mouth, this time accompanied by Kyubey. The movie's title sequence begins.
On the way to school Madoka is greeted by Sayaka and Kyoko. Kyoko is now a student in Madoka's class, though she is a bit of a slacker. The three of them discuss school and homework. In class, Kazuko rants about the world possibly ending before introducing the transfer student, Homura. Homura is once more wearing her glasses and braids. While Kazuko is continuing her introduction, Homura deliberately shows off her ring, revealing to Madoka, Sayaka and Kyoko that she's also a magical girl. Later in the day the girls speak with Mami. Mami admits that she already met Homura and wanted to surprise the others. Homura explains that she helped them in the nightmare battle they had last night. The other magical girls quickly welcome Homura into their group.
Later, Homura and Madoka discuss how it's been a month since Homura arrived. They admit it feels like they've always been together while at the same time feeling that they have been waiting forever to spend time with each other. Meanwhile, Hitomi calls Kyosuke from her room in order to ask if he's available over the weekend. Kyosuke admits that he has to practice for an upcoming recital. Hitomi initially seems understanding after ending the call, but then she flies into a rage. Red threads come out of Hitomi's bed before it seems to swallow Hitomi. Hitomi's nightmare emerges.
At Mami's house, Bebe announces the presence of the nightmare. Sayaka and Kyoko go to the nightmare first and recognize it as Hitomi's. Sayaka jokes that Hitomi must have it hard with Kyosuke as her boyfriend and says that she knows because she has "life experience". The other magical girls arrive to join them and they all transform. The girls announce themselves to be the "Puella Magi Holy Quintet" (the first time any character has spoken the words "puella magi"). The nightmare attacks, but it is quickly contained by the magical girls. Bebe places a cake container around the nightmare and transforms into her alternate caterpillar form. The characters sing the Cake Song, which turns the nightmare into a cake. Bebe then eats the cake whole and spits out a blob shaped like Hitomi's head. Sayaka catches the blob as well as a falling piece of paper with a picture of a violin on it. Sayaka throws the paper into the air and it turns into a silhouette of Kyosuke playing the violin. The Hitomi blob flies up after it and vanishes, releasing sparkles that purify the magical girls' soul gems. Hitomi reappears sleeping beside her bed, while the city returns to normal. The characters celebrate their victory, but Homura feels something is wrong.
The next day, Homura notices that almost all the teachers and students at her school have distorted faces. Later, while sharing a meal with the other magical girls, Homura sees that everyone in Mitakihara has the same distorted faces. The scene switches to a bunch of girls in strange outfits watching an organ grinder; these girls reappear throughout the film. It's then shown that Homura is having a personal meeting with Kyoko where she tells Kyoko about her suspicions. In fact, Homura says that she came to Kyoko because she felt that there was something wrong with the way Kyoko was acting, which made her different from everyone else. Homura asks Kyoko where she lives and when she started coming to Mitakihara Middle School. Kyoko says that she's staying with Sayaka and she transferred to the school before Homura did — but she doesn't remember when. Homura then asks where Kyoko lived before coming to Mitakihara. Kyoko says she came from Kazamino City, which is next to Mitakihara. She says that she came to Mitakihara because Kazamino wasn't having any problems and Mami needed help. Homura asks Kyoko to take her to visit Kazamino. Kyoko agrees, on the condition Homura treat her to ramen afterward.
The two girls ride a bus to Kazamino, but are shocked when the bus returns to Mitakihara without stopping. To ensure they didn't get on the wrong bus, Homura and Kyoko take the next bus to Kazamino, but find that it has suddenly become a Mitakihara local bus. They try walking to Kazamino directly, but find themselves back where they started. Kyoko realizes that something is trapping them in Mitakihara and pulls out her soul gem. Homura stops her from transforming and tells her that there might not even be anything outside of Mitakihara. She asks Kyoko to keep it a secret from the others. When Kyoko protests, Homura tells her it's safer to pretend nothing is wrong. Both girls are suddenly surrounded by wobbly humans with odd faces. Homura advises Kyoko to let her handle it. Kyoko relents, and the odd humans walk away. Homura says that whoever is trapping them won't do anything as long as they don't try to escape. Kyoko agrees and admits that something is off with her memories. She says that although Homura is acting more confident, it doesn't feel strange at all. In fact, she feels Homura is acting the way she is supposed to. Kyoko then leaves, while Homura walks off in the opposite direction. Homura pulls off her braids and glasses and remembers that she's seen something like this before: An illusionary space that traps human victims in a labyrinth. Homura concludes that this Mitakihara City is actually a witch's barrier.
Homura wanders through flashbacks from the original anime as she muses to herself about witches. She remembers the time loop she was in, which was broken by Madoka's sacrifice. She concludes that the witch has altered everyone's memories to trap them in the fake Mitakihara. Later, Homura has tea at Mami's apartment with Mami, Madoka, and Bebe. Madoka and Homura both ask about when Mami met Bebe. Mami says that she met Bebe before meeting Madoka and Sayaka — though she doesn't remember how they met. However, Mami admits that Bebe used to be the only one supporting her, and without Bebe she would have fallen into despair. Bebe walks up to Mami and jumps into her lap, indicating she reciprocates their friendship. Mami admits that she used to act like the dependable senior, but now she's surrounded by people she can depend on. Bebe says that Mami's really a crybaby, causing Mami to laugh. Madoka and Mami muse that nightmare hunting is almost like a happy dream now.
Homura asks Mami for another cup of tea. As she leaves the room, a ribbon can briefly be seen trailing behind Mami. Once Mami leaves Homura transforms and stops time. She then grabs Bebe, unfreezing her from the stopped time. Homura says she recognizes Bebe as Charlotte and accuses her of being the witch that created the barrier. Bebe claims not to understand what Homura is talking about. Homura leaves Mami's apartment, recalling the difficulties she had with Mami in the past. Homura tries to interrogate Bebe further, but then one of Mami's ribbons appears tied around Homura's leg. Homura is then confronted by Mami, who has the other end of the ribbon wrapped around her arm. By holding onto the ribbon attached to Homura, Mami is immune to Homura's time stop and has been observing her the whole time. She demands Homura explain herself. Homura claims that Bebe is deceiving her, that their memories are fake, and that the city of Mitakihara is an illusion. Mami doesn't understand what Homura is talking about, prompting Homura to unfreeze time, throw Bebe in the air, and shoot at her. Mami pulls Bebe away with another ribbon and tells her to escape. Homura stops time again and tries to shoot off Mami's ribbon, but it dematerializes before the bullet hits. Homura asks Mami if she's willing to protect Bebe. Mami says she is, and the two girls proceed to have a gun duel as Homura freezes and unfreezes time.
After a frantic battle, both girls prove to be evenly matched. With time still stopped, Homura puts a gun to her head, as if she were attempting to kill herself. A shocked Mami pulls on the ribbon tied to Homura's leg, tripping Homura. However, this turns out to be just as planned; Homura fires the gun through her head and wraps the ribbon around the bullet. The bullet breaks through the ribbon, severing Mami's connection to Homura and freezing her in time. Homura gets up and aims her gun at Mami's soul gem, but decides to incapacitate Mami instead by shooting her leg. The bullet stops before it hits Mami. Homura unfreezes time, the bullet connects, and Mami breaks apart to reveal a mass of ribbons. Homura is entrapped by the ribbons and is confronted by the real Mami. Mami says that since Homura didn't try to hit anything vital she must care about her in some way, but she demands to know why Homura attacked Bebe. Homura insists that Bebe's a witch, the enemy of magical girls. Mami has no idea what a witch is, and says their enemies are wraiths. Mami's statement shocks both herself and Homura. Mami remembers that they've always been fighting against wraiths, and then wonders what the nightmares are. Mami's recollections are disrupted by a giant mouth opening up in the sky. Suddenly a fire extinguisher falls from the sky and is stabbed with a sword, covering everything in smoke. When Mami blows the smoke away she finds Homura is gone. As Mami wonders what is going on, a voice comes from behind her saying she can explain. Mami turns to see a new magical girl, Nagisa Momoe, and realizes that she's Bebe. Nagisa apologizes for deceiving Mami and asks her to stay calm and listen.
It's revealed that Homura was rescued by Sayaka, who breaks Homura out of her bindings. Sayaka chides Homura for fighting Mami and for suspecting Bebe as the culprit just because she was a witch. Homura is surprised to find Sayaka remembers witches. Sayaka admits it's her role, and then says that the Charlotte Homura remembers wasn't the sort of witch who could create a replica of Mitakihara and trap the others in it — especially since the witch hasn't attacked anyone. Sayaka explains that the witch's barrier isn't a trap to lure in prey, but a world the witch wants for herself. She rhetorically asks Homura who benefits from the barrier. Homura then attempts to stop time, but Sayaka thrusts her sword into Homura's shield and prevents the time stop from occurring. Sayaka chides Homura again for relying too much on her time powers, which bothers Homura because Sayaka is implying she has knowledge of prior timelines. Homura says that the witch must be one of the five magical girls. Sayaka confirms this, and asks Homura what she will do if she finds the witch. Homura says the answer is obvious: she'll destroy it.
Sayaka asks if this world where everyone is happy is wrong, and if the heart who wished for this world is bad enough that it needs to be destroyed. Homura asks Sayaka if she's defending the witch. Sayaka admits that she has to sympathize with them, since magical girls become witches. Homura then remembers something important: the reason Mami doesn't remember witches is because witches no longer exist. She remembers Madoka's sacrifice prevented witches from being created, and magical girls are now taken by the Law of Cycles. Homura says there are three things that shouldn't exist: The witch that created the barrier, Bebe who is in the form of a witch, and Sayaka with her knowledge of witches. She demands to know who Sayaka is. Sayaka simply says that she's exactly who Homura thinks she is. Suddenly Oktavia von Seckendorff's reflection appears in the puddle the girls are standing on. A shocked Homura attempts to stop time and is once more blocked by Sayaka. She knocks away Sayaka's sword and kicks her backwards. Sayaka throws her cape over herself just as Homura stops time. Homura points her gun at Sayaka's cape, which has grown larger and has an image of Oktavia on it. Homura pulls on the cape and unfreezes time to reveal that Sayaka has vanished. Sayaka's voice, seemingly coming from everywhere, tells Homura that she hasn't answered her question about the witch who created the barrier. Sayaka tells Homura to think carefully before destroying the false Mitakihara, so she doesn't leave behind any regrets. The cape blows away in the wind.
Homura travels on a boat through the false Mitakihara. Animated drawings of Kyoko, Mami, and Sayaka repeat lines from earlier in the movie. She thinks that whoever is responsible for creating the barrier has abandoned the responsibility of fighting wraiths and escaped into this perfect world, which Homura believes is unforgivable. We then see a scene of Homura kneeling before a picture of Ultimate Madoka. Behind Homura are the oddly dressed girls, who are eating pomegranates. Homura claims that fighting wraiths is the price magical girls pay for their miracle, and that Madoka sacrificed herself for the sake of all magical girls. The boat is seen ablaze and sinking. Homura says this farce is just making light of Madoka's sacrifice, and she won't forgive it. Homura is shown sliding her hands over the picture of Madoka, while the oddly dressed girls throw their pomegranates, shouting "Gott ist tot" ("God is dead"). The boat reappears with Homura on it. As it passes under a bridge, Madoka and Kyubey appear and leap onto the boat from the bridge. Madoka expresses relief at finding Homura, and asks what happened to her. When Homura has difficulty answering, Madoka tells her it's no good to be all alone. As they walk through the city, Madoka admits she could listen to Homura's problems, even though she feels she might not be of any help. They walk to a flower field, where Madoka says that it hurts her if she can't help Homura.
Homura says she had a "dream" where Madoka went to a place so far away that she could never see anyone again, yet Homura was the only one who remembered Madoka was gone. Homura falls to her knees and admits that no-one could understand her feelings, and she began thinking that her memories of Madoka were something she made up. Madoka embraces Homura and says that sounds like a truly scary dream. She then tries to reassure Homura by telling her that she would never go far away like that. Homura asks how Madoka can say that for sure. Madoka says it's because she's her, and she could never handle something that would make Homura cry. Homura is surprised by this, and asks if it was also too painful for Madoka to bear. Madoka agrees, and says she could never abandon her friends and family; even if she had no choice, she feels she could never be strong enough to do it. This is shown to be a major revelation to Homura, who exclaims that if this is how Madoka feels then she's made a terrible mistake. Homura says she never should have accepted Madoka's sacrifice, and should have stopped Madoka from sacrificing herself. Homura tells Madoka that she is brave enough to make the decision to abandon her friends and family, and says that Madoka is much kinder and stronger than she realizes when she knows there's something only she can do. Homura says that Madoka doesn't seem to remember anything, and that she initially thought Madoka might have been an illusion. She explains that she now realizes Madoka is real, and just being with Madoka again has truly made her happy. Homura gets up and says she has something to do. She then leaves Madoka and Kyubey behind in the flower field.
Kyoko is shown getting a cellphone call. She is no longer wearing her school uniform and is at the arcade, suggesting she has returned to her old habits. The call is from Homura, who asks Kyoko if she remembers anything about witches. Kyoko doesn't know what they are, and asks if that's a problem. Homura says that not knowing is the right answer. Homura then asks Kyoko if she remembers Madoka. Kyoko says she does. Homura says there isn't any reason Kyoko should know about Madoka, and those memories must be fake. Homura claims that she should have figured out the truth earlier: The only person who could create a world where Madoka exists is someone who knew about Madoka in the first place. Homura proceeds to get on the bus to Kazamino while leaving her soul gem behind. Kyoko runs out of the arcade, asking if Homura's alright. She then looks up and sees a blimp on fire that's falling from the sky right at her. Unaware of the crashing blimp, Homura says there's only one more thing she needs to confirm before ending everything. She apologizes for involving Kyoko, turns off the cell phone, and drops it. Homura reveals her plan is to see what happens to her when she's too far from her soul gem. Homura soon finds that nothing happens to her at all. Fire erupts from inside the bus and the windows blow out. Meanwhile, blimps begin crashing all over the false Mitakihara. The city goes up in flames as bizarre objects rise from the ground. The bus suddenly falls out of the sky, crashes into the ground head-on, and explodes near the place where Homura left her soul gem. Homura reappears unharmed, and says she is no longer a magical girl. She shoots and shatters her own soul gem, without consequence. The girls in strange outfits reveal themselves to be familiars. Homura must now accept the truth: she has been the witch all along.
A cocoon shaped building rises from the ground below Homura and flies into the sky. Kyubey appears within the building, chides Homura for pursuing a truth that she does not desire, and claims human curiosity is irrational. It becomes apparent that his previous persona was just an act. Homura reappears wrapped in a white blanket. She throws it off to reveal she's now wearing a black dress, and says that she figured Kyubey was responsible. Kyubey reveals that Homura's body is outside of the barrier, while her soul gem is trapped in an "isolation field" — a space created by the incubators that blocks out any external influence. In fact, the incubators are using Homura as part of an experiment to see what happens to soul gems when they go completely black. The isolation field even prevents the Law of Cycles from acting on Homura's soul gem, causing it to form a barrier — which Kyubey recognized as a power of the witches Homura told him about. (This implies that Homura's discussion with Kyubey at the end of the anime is what led to the experiment. It also implies that the isolation field is actually blocking Madoka's omniscience, since she cannot enter the isolation field as a concept.) Kyubey explains the isolation field is preventing Homura from fully becoming a witch, comparing her to a chick that grew inside her egg without breaking it. The barrier, including the false Mitakihara, is actually within Homura's soul gem. When Homura questions how people came to be trapped inside the barrier, Kyubey explains they made an adjustment that allowed things to be "invited" inside. Images of the familiars appearing in the real world behind Mami, Kyoko, Hitomi, and Kyosuke are shown, implying they abducted the victims and pulled them into the barrier. Kyubey explains that the people trapped in Homura's barrier are people that Homura subconsciously wished for. Futhermore her barrier could also invite the Law of Cycles itself, which would allow the incubators to observe what causes the disappearance of magical girls when they run out of magic. Kyubey has deduced that the Law of Cycles is already present in Homura's barrier, and it has materialized as a girl who never existed: Madoka Kaname. However, she has not displayed any unusual abilities. Kyubey believes that Homura's barrier has altered Madoka's memories as well, causing her to forget she was a god the same way Homura forgot she was a witch. He asks Homura to call out for Madoka's help, which would restore Madoka's memories and return her power as the Law of Cycles.
Homura asks Kyubey what his goal is. Kyubey says his kind wants to observe the Law of Cycles, which to them had only been a hypothesis. Homura insists on knowing why, claiming that if Kyubey considers curiosity irrational, he wouldn't go through all this trouble merely to observe something unknown. Kyubey doesn't answer, but Homura realizes that his goal is to control Madoka and attacks Kyubey with her witch powers. Kyubey evades the attacks and admits that by observing the Law of Cycles the incubators could interfere with and control it. This would allow them to turn magical girls into witches, reinstating the old system that provided the incubators with more energy. He tells Homura that she shouldn't be mad because her existence is at an end, and says she should be happy because she'll soon reunite with Madoka. Homura says that is not the happiness she wished for and begins filling her heart with grief, filling the tower with black liquid and accelerating her own transformation into a witch. Kyubey exclaims that if she transforms, she won't be able to be purified. Homura says that her wish was to save Madoka, and she would become a witch if it means keeping Madoka away from the incubators. Kyubey asks if Homura wants to spend eternity trapped inside her barrier as a witch, but Homura believes that Mami and Kyoko will kill her instead and allow her victims to escape. Kyubey says that this means Homura won't be saved by the Law of Cycles, and she won't ever see Madoka again. Homura tells Kyubey to shut up, and her powers and familiars begin killing Kyubey repeatedly. Kyubey eventually escapes the building as a shape arises from the liquid.
Suddenly, Homura is shown sitting in a chair next to Madoka (a reference to the opening sequence of the first two movies). Madoka suddenly gets up onto the chair, falls to the ground, and collapses into a puddle. Homura tries to stop Madoka but fails, and distorted versions of Homura look down on her. Homura is then crushed by a giant version of herself pounding her hand into the ground.
It's then revealed that Homura has now turned into her witch form, Homulilly. Homura muses to herself about becoming a witch, and as she breaks out of the cocoon building part of her head falls off. She begins to march out of the cocoon along with her familiars. In her mind, she thanks Madoka for coming to see her, and apologizes for not being able to say goodbye. A countdown similar to the one Walpurgisnacht had in episode 11 appears, ending with Homulilly and her familiars marching towards a guillotine.
From afar, the other magical girls and Bebe watch Homulilly's procession. Sayaka tells everyone not to be afraid, and that Homura is suffering more than anyone else. Kyubey appears and asks if they're really going to fight Homura. Kyoko calls Kyubey out on suddenly talking, and Mami says they have to believe what Bebe told them. Kyubey tells Madoka that she can save Homura if she just remembers her own powers, but Sayaka tells her not to listen and to follow their own plan. Bebe transforms back into Nagisa and uses her weapon, a horn that blows explosive bubbles, to blow cracks into the ceiling of Homulilly's barrier. Homulilly's familiars charge towards the magical girls. In response, Sayaka stabs herself to summon Oktavia and an army of familiars from other witches. Nagisa and Sayaka explain that they are magical girls freed from karma by the Law of Cycles, and have now become a part of it (Sayaka says that they're like "secretaries"). It's revealed that Madoka, Sayaka, and Nagisa didn't have their memories altered by Homura's barrier. Instead Madoka entrusted her memories and powers to Sayaka and Nagisa in order to fool Kyubey. Sayaka and Nagisa simply played along with the barrier while waiting for the right time to reawaken Madoka. Sayaka admits that while it's caused them quite a bit of trouble, Homura has been trying hard and deserves her reward.
The movie's climactic battle begins. Homulilly's charging Lotte familiars are met by an army of Anthonys. Nagisa partially transforms into Bebe and devours several Luiselotte familiars, releasing another stream of bubbles from her head. Oktavia holds off Homulilly while Madoka and Mami swing on trapezes. Madoka shoots an arrow into the barrier's broken ceiling, prompting Homura to beg everyone to stop. Homulilly sends out her elite familiars, the Clara dolls, who tear right through the Anthonys' lines. Madoka rescues Nagisa from the Clara dolls, which are held off by Mathieus, before Madoka and Nagisa ride past them on a Sebastian. Sayaka battles one of the Clara dolls, but another one knocks her into the air where she is swallowed by a giant Liese familiar. Kyoko destroys the familiar and saves Sayaka, muttering about being dragged into something that doesn't make any sense to her. She then tells Sayaka she had a horrible dream where Sayaka died, but admits realizing that the dream was actually reality, and the world they're in now is actually the dream. Sayaka says it's not a sad thing for Kyoko to call this world a dream. She tells Kyoko that while she first thought she had no more regrets, she took on her duty because she had one regret after all: leaving Kyoko behind. Nagisa butts in and says she came back because she wanted to eat cheese again, prompting Sayaka to yell at her for ruining the mood. Sayaka and Kyoko then fight off the familiars together. Several giant Lottes attack Nagisa, while Madoka's arrow shots are blocked by shields with mouths. Mami swings onto a cake tank on rails and fires a giant Tiro Finale, destroying Homulilly's defenses (and accidentally sending Nagisa flying). Oktavia then uses Kyoko's spear to punch another hole into the barrier. Finally, Madoka shatters the barrier's ceiling with one final arrow shot, revealing Kyubey's isolation field. Sayaka explains that if the isolation field is destroyed, Madoka can finally save Homura without interference.
In Homura's mind, she has flashbacks to the end of timeline 3 where she killed Madoka and also has visions of being killed by herself. Suddenly Madoka calls to Homura, saying that she told Homura not to be alone. A window opens and a scarred hand comes out of it. Madoka says Homura is Homura, no matter what happens, and she won't ever abandon her. Homura's mental representation takes the hand and apologizes for being a coward and betraying her desire to see Madoka again. As she returns to normal, she claims that she can bear any sin and be reduced to any form, because as long as Madoka is by her side she'll be fine. Madoka and Homura reappear atop Homulilly's broken head, and they put their bows together for one final attack. As they charge the attack, Madoka asks if Homura is scared. Homura responds that she's fine, and she won't hesitate anymore. They release the attack, which pierces through the isolation field and launches a rain of arrows upon the assembled incubators. As their bodies are destroyed the incubator exclaim their surprise in unison.
The barrier vanishes, revealing a place that appears to be the location Homura was in at the end of the anime. Mami places Homura's soul gem on her body. A few familiars assist the remaining victims (Kyosuke, Hitomi, Kazuko, Nakazawa, and the Kaname family) who are all asleep. Finally, Kyoko asks if Sayaka and Bebe are gone. Mami says they aren't, and they'll be taking Homura with them at last. A light appears in the sky. Kyoko asks if it's Madoka. Mami says it is, and that one day she will be coming for them. Ultimate Madoka descends from the sky, along with a carriage led by a Pyotr riding Walpurgis Night's elephant. The carriage contains Sayaka and Nagisa. Homura opens her eyes and sees the carriage, Kyoko watching with Mami, and finally Madoka coming for her. (In other words, Madoka has unlocked her full powers and is observable.) Madoka, who is regaining her memories, apologizes for making Homura wait and says it's time for them to be together forever. As Madoka reaches down for Homura's soul gem, Homura says that she was waiting for this moment. She then grabs Madoka's hands, surprising her. (It is implied that Madoka has not regained her omniscience because she is still existing in only one place.) Homura says that she's finally caught Madoka as her soul gem goes completely black. Darkness spills out of her soul gem as a swirl of colors appear in it. Nagisa calls it a color worse than curses. Sayaka asks Homura what she is doing. Homura says that she doesn't expect anyone to understand, and that her feelings belong only to her and are meant for Madoka only. Reality itself begins to crack. Madoka begs Homura to stop or she'll be torn apart. Suddenly Madoka is separated from her goddess self. As reality cracks further, Homura embraces the human Madoka and says she'll never let go of her again. Finally, the colors spill from Homura's soul gem, engulfing all the characters. The cracks spread throughout the universe, followed by the colors from Homura's soul gem.
Homura appears floating in the void. Her soul gem emerges from her mouth, and she shatters it. The dark orb appears and flies into her hand. Kyubey appears, claims the world is being rewritten, and asks if a new concept is being born into the universe. Homura explains that this is the second time she's seen this place (the first was after Madoka's ascension at the end of the anime). Kyubey asks Homura why her soul gem hasn't vanished. Homura says she remembered how many timelines she repeated and the suffering and pain she experienced all while thinking of Madoka. She says that even the pain is now dear to her. What tainted her soul gem was no longer a curse, but something the incubators could never understand. As she swallows the dark orb, she claims it is the pinnacle of human emotions, something more passionate than hope and deeper than despair: Love. Kyubey says Homura is no longer a magical girl or a witch, and asks what she is becoming. Homura transforms into a new costume and grows a pair of black wings. Homura says that since she is a being that brought down and imprisoned a god, it's only appropriate to call her a demon. Kyubey exclaims that his kind never should have experimented with human emotions, as this is a result they can't handle. Kyubey attempts to run away but Homura, now a giant, catches him. She claims that she still needs his existence to deal with the world's curses, and says she'll make Kyubey cooperate.
The setting changes to Earth. Homura sits at a table on the middle of the road to Mitakihara Middle School. She is apparently unnoticed by any passersby. A Pyotr appears briefly but vanishes. Mami, now in her school uniform, holds out her hand to catch falling cherry blossoms. Homura reaches her hand forward and knocks over a teacup. Mami turns around, but sees no-one behind her. She finds that she's caught a black feather. Elsewhere, Kyoko (also wearing her school uniform) is on a tree, feeding an apple to some Liese familiars. A group of Clara dolls wave their arms at Kyoko from the ground. Kyoko throws another apple at them, but Homura shakes her head and the apple falls into the water. Kyoko looks up shocked as the Lieses, now apparently normal birds, fly out of the tree. She looks down on the road, but finds only students going to school. The apple floats down the river and is chased by the Clara dolls. Finally Sayaka appears before Homura and confronts her. Sayaka angrily says that Homura has taken away the Law of Cycles. Homura, now wearing an earring and lacking her magical girl ring, claims she only took a part of the Law of Cycles — the part that was Madoka before she stopped being herself. She says that somehow Sayaka and Nagisa are now trapped in the real world and are unable to return to where they were. Sayaka asks what right Homura has to do this. Homura says that as a demon, it's only natural she goes against god. As she's saying this, some of the Clara dolls appear to be committing suicide by throwing themselves off a bridge. Sayaka asks Homura if she plans on destroying the universe as Oktavia rises from the water behind Sayaka. Homura supposes that's a fine idea after all the wraiths are destroyed. She says when that time comes she'll gladly be their enemy, but then asks if Sayaka can oppose her when her memories are being altered. Homura claps her hands and Oktavia disappears, causing Sayaka to stumble. Nagisa suddenly appears in her civilian outfit, running around happily. Sayaka says she was a part of something bigger, and was somewhere else, but she can't remember what it was like. Homura says Sayaka should be happy about being able to return to her human life, and that eventually she won't feel out of place anymore. Sayaka says she won't forget the fact that Homura Akemi is a demon. As the Clara dolls throw tomatoes at Homura, she tells Sayaka to at least try to get along with her so "that girl" won't be mad. Suddenly Homura vanishes. Nagisa runs to some other children her own age and they leave, while Sayaka is then greeted by Hitomi and Kyosuke. Even though she doesn't remember, Sayaka begins tearing up and says that somehow being greeted by her friends makes her feel very happy. Hitomi claims Sayaka always says strange things, and Sayaka agrees with a laugh. We see that she still has her magical girl ring and soul gem tatoo, but the runes on the ring have vanished.
Class begins for Mitakihara Middle School as Kazuko rants about her love life again. Homura is sitting at her desk looking bored. Suddenly Kazuko introduces a new transfer student: Madoka Kaname, now wearing yellow ribbons (seen in the anime's first episode). Madoka explains that due to her mother's job, her family has spent the past three years living in America. Madoka is swarmed by classmates asking her questions, but Homura stops them by saying they're bothering Madoka. She then introduces herself to Madoka and offers to give her a tour of the school. As Homura walks ahead of Madoka, she asks how coming back to Mitakihara feels. Madoka says it feels familiar, but something seems different. Homura says it's understandable, but then Madoka says that Mitakihara hasn't changed — it's herself. Madoka's eyes turn gold, prompting Homura to turn around in shock. Madoka says she's sure she had a different form and purpose. Reality changes as her hair ribbons vanish. Just as it seems she's about to change into Ultimate Madoka, Homura grabs her from behind which returns Madoka and reality back to normal. Homura claims that Madoka is her true self. Homura then asks Madoka if she considers the world precious and if she thinks laws or desires are more important. Madoka says she thinks laws are more important, and think it's a bad thing to just selfishly break the law. Homura takes off her hair ribbon (which she initially received from Madoka) and says that Madoka might become her enemy someday. As she ties the ribbon back into Madoka's hair, Homura says she doesn't care, as she only wants a world where Madoka can be happy. Homura then says the ribbons suit Madoka better. The last sequence before the credits is a montage. Sayaka and Kyoko are enjoying Pocky together, some Anthonys are seen passing roses, Mami rescues Nagisa from falling boxes of cheese, and Madoka is unpacking with her family.
After the credits, Homura is seen sitting on a chair at the edge of a cliff. The moon is apparently broken in half. Suddenly Homura hears the sound of plants rustling. She turns to look in surprise, and sees Kyubey pop out of the foliage, which seems to disappoint Homura. The dark orb appears from Homura's hand and she begins dancing with it. Kyubey reappears suddenly looking disheveled. Homura grabs the dark orb in her hand, smiles, and apparently falls over the cliff. Kyubey is seen again, quivering. A close-up of his eye reveals that darkness is swirling around in it. Finally the word "END" appears in different languages. The movie ends with a closed window, tied shut by a ribbon.