Refusing to let Homura's efforts go to waste nor allow Magical Girls everywhere to live in despair, Madoka comes up with the perfect wish that rewrites the laws of the universe. Once the wish is complete, Homura is left in the new world without her best friend.
----
!!Tropes in this episode include:
* AllForNothing: While stuck in a void of time and space, Homura believes that her efforts were for naught given Madoka's RetGone. Though her best friend comes to assure her that it wasn't.
* AndTheAdventureContinues: Even though Madoka rewrote reality for the better, there are still monsters of despair (Wraiths) who wreak havoc on the world giving all Magical Girls an incentive to keep on fighting. And not wanting to let her best friend's efforts be for naught, Homura vows to keep on fighting until they meet again.
* AsYouKnow: Mami reminds Kyoko that when a Magical Girl's Soul Gem becomes full of despair, it suddenly disappears along with the Magical Girl it was tied to. This phenomenon is known as the ''Law of Cycles''.
* AscendToAHigherPlaneOfExistence: Madoka's efforts in saving all Magical Girls while carrying their curses turns her into the new God of Magical Girls. This grants her advanced powers and also the ability to see every world that has ever been and ever will be.
* BadassBoast: As Homura weeps for her friend who became a Witch that plunged the Earth with never-ending curses, a voice offers her assurance.
-->'''Godoka:''' No, it's alright. Remember? I wished for the power to erase all Witches. And if what I wished for really did come true, then even ''I'' have no reason to despair, ''ever''!
* BackFromTheDead: Since their deaths were caused by Witches, Mami and Kyoko are able to live in the new world.
* BeCarefulWhatYouWishFor: All this time Kyuubey hounded Madoka into making a contract with her promising that her potential will guarantee any wish of hers to come true. This comes back to bite him hard as he's forced to comply with Madoka's wish to erase all witches which ensures a better outcome for the Magical Girls he victimized for eons. To add insult to injury (not that Kyubey can remember enough to know this), the new universe's rules mean that the Incubators are actually gathering energy at a slower rate than they were in the previous one. While they're still gathering energy to hold off entropy, it's not at a pace that they particularly like.
* BittersweetEnding: Thanks to Madoka’s wish, Walpurgisnacht has been defeated, there are no witches, there never will be, and there never have been, magical girls are carried off to Magical Girl Heaven instead of turning into witches, Incubators are able to gather curse energy harmlessly, and both Kyoko and Mami return from death. Madoka is a goddess, and one day, she and Homura will be together again. On the bitter side, the magical girls fight wraiths (rather than witches), Sayaka is still dead (though at least this time it was while fighting wraiths alongside her friends), and Madoka has disappeared from normal existence, forgotten by all except Homura and Madoka's pre-verbal little brother (whom WordOfGod states will eventually forget her as well).
* BookEnds: The first episode featured Junko picking out a set of ribbons for her daughter to wear. Near the end, Junko sees Homura's ribbons and states that she'd have her daughter (if she ever had one) wear them.
* CallBack:
** Kyoko applauds Madoka for finding her reason to fight like a Magical Girl.
** Mami also returns her sketchbook with her Magical Girl fanart.
* TheCameo: An Anthony is petted by Godoka just before she destroys her other self.
* DeadPersonConversation:
** Just before beginning her universal salvation, Madoka has a final chat with Mami and Kyoko over what's to come.
** Madoka also talks with Sayaka while attending Kyousuke's performance.
* DeclarationOfProtection: Madoka has these words for the white rat when it questions if she intends to become a god.
-->'''Madoka:''' I don't care what I become. All the Magical Girls who believed in hope and fought Witches, I don't want them to cry or suffer anymore. I want them to be at peace. And if that goes against the laws of the universe, [[BadassBoast then I'll just rewrite those laws]]. That's the only thing I want. It's what I wish for. [[DidYouJustFlipOffCthulhu Now! Grant my wish, Incubator!]]
* DisappearsIntoLight:
** This happens to Madoka once she ascends into heaven leaving Homura behind.
** It happens again to her and Sayaka during Kyousuke's performance when the latter is ready to move on.
* EmbodimentOfVirtue: Mami declares that Madoka will become the hope of every Magical Girl. And she lives up to that title by giving hope and peace to every Magical Girl in existence.
* TheEndOfTheWorldAsWeKnowIt: Madoka's Witch form Kriemheild Gretchen returns as a cosmic monstrosity capable of plunging the world into eternal damnation with it's cumulated curses. Fortunately, Godoka puts an end to her.
* FairyTaleMotifs: Sayaka's [[{{Literature/TheLittleMermaid}} Little Mermaid story]] ends just as the fairy tale, with her ascending to a higher plane and is more at peace compared to when she died from heartbreak.
* FateWorseThanDeath: Mami warns Madoka that she'll spend all of eternity fighting curses before essentially fading from existence. She considers death to be a kinder fate than that.
* HistoryRepeats: Walpurgisnacht is once again defeated by Madoka, only this time by the power of her hope.
* InMediasRes: The beginning of the new order starts with Madoka reuniting with Homura during Walpurgisnacht's rampage.
* InSpiteOfANail: Despite Madoka's efforts, Sayaka ''dies'' after she falls into despair with Kyoko expressing grief over her death.
* LeaningOnTheFourthWall: While talking with Homura about the name Madoka, Junko mentions that it sounds like something from an anime show.
* LoopholeAbuse:
** As a time traveler, Homura's magic allows her to witness the transformation of the old world in favor of Godoka's new world order.
** Madoka's wish made it so that no Magical Girls would ever fall into despair and turn into a Witch. And that includes ''her''.
* NoBodyLeftBehind: After Madoka successfully purifies any given Soul Gem, while making the Gem disappear, the Magical Girl fades away into heaven.
* OhCrap: Kyuubey is flabberghasted with Madoka's wish and how it'll unravel the fabric of reality.
* TheOmniscient: As the new God of Magical Girls, Madoka has been able to see every world that has ever been and ever will be. Because of this, she at last learns how much Homura suffered and endured in her hope of saving her.
* OurGhostsAreDifferent: Now that witches have disappeared, a new harbinger of despair known as Wraiths have taken form in the new world. They resemble giant white ghosts with pixelated faces who feed on human suffering. Defeating them grants Magical Girls a means of cleansing their Soul Gems.
* RetGone: The ultimate price Madoka pays for her wish is that her very existence is erased. No one apart from Homura will fully remember her and she'll be separated from her loved ones forever.
* SacredBowAndArrows: Madoka regains her bow and arrows when she transforms. And with a single arrow, she launches an eternal array of arrows that reaches Magical Girls on the brink of despair throughout the universe and history itself.
* SayMyName: Homura screams out her best friend's name just before they're forcibly separated.
* TitleDrop: In the void of time and space, Madoka refers to Homura as "My very best friend".
* TragicKeepsake: Just before they're separated, Madoka gifts Homura her red ribbons. Homura would wear these after returning to her new world.
* IWantMyBelovedToBeHappy: Thanks to her old friend's intervention and seeing the true beauty of her healing wish, Sayaka is able to make peace with Kyousuke falling in love with Hitomi.
* WhamLine: Taking a breath of faith, Madoka makes her wish.
-->'''Madoka:''' I wish I had the power to erase witches before they're born. Every single witch, from the past, present and future. Everywhere.
----