As a very general rule, it can be said that while traditional drama begins sad and ends happy (a problem introduced early on is solved by the end), tragedy begins happy and ends sad (the tragic hero’s fatal flaw leads to his fall from grace). If one looks at the first eleven episodes of Madoka, it’s clear that the story began happily but from the end of episode 3 onwards, the show becomes increasingly darker. At the end of episode eleven, the audience is left wondering what Madoka’s wish will be with all of the knowledge about the truth and history of Magical Girls she now possesses. Given the show’s emphasis on maintaining the karmic balance between good and evil, wishes and curses, the creators would be betraying the integrity of the show if they found a way for Madoka to solve all of the problems without any consequences. At the same time, it would be a betrayal to have Madoka make a wish that destroyed Walpurgis Night but also led to Madoka dying or becoming a witch since the audience had already seen those outcomes in Homura’s past. This could only be pulled off if the creators wanted to emphasize the futility of fighting fate and really deliver a soul-crushing bummer ending. Based on these observations, the creators needed to deliver an ending that maintained the karmic balance and led to some sort of consequence while solving the most pressing problems facing the characters in an unexpected and satisfying way. And boy does writer Gen Orobuchi deliver.

I personally have a difficult time thinking of a better way this series could have ended. By wishing to destroy all Witches past, present, and future with her own hands, Madoka found a way to solve the immediate problem of Walpurgis Night wrecking her town and the more universal problem of magical girls becoming Witches. However, this reality-altering wish isn’t without its consequences as Madoka is eliminated by her transformation into a witch and its subsequent paradoxical destruction by her own hand. She never existed as a person and instead becomes an intangible force, a principle of the new universe. As Mami points out in episode 12, in many ways “death would be a kinder fate”. Thus we fulfill the requirement of solving the most pressing problems facing the characters while having significant consequences for Madoka, the wish maker.

The wish also stays within the limits of karma and balance set earlier in the series. Evil and curses still exist in the world, they just take a different form as the Wraiths. As powerful as Madoka is, she can’t change human nature and extinguish all evil without simultaneously extinguishing free will. Being a Magical Girl still means giving up your soul and resigning to a life of never ending battle. The difference is now when a Magical Girl gives into despair and her wish reaches the climax of the good it will provide to the world, she passes on instead of becoming a witch and creating more despair. This is illustrated by Sayaka’s fate. Madoka admits she could have saved her, but doing so would require her to alter Sayaka’s wish. Instead of turning into a Witch, Sayaka passes away after using up the last of her energy, succumbing to what Mami calls “The Law of Cycles”. Through Madoka’s sacrifice, the balance of the universe is maintained while eliminating the existence of witches.

The final part of my criteria about the ending being “satisfactory and unexpected” comes down to personal opinion. However, I would argue that by so neatly wrapping up all the other criteria without compromising the integrity of the series both surprised and satisfied me as a viewer.

Now, could Madoka’s fate have been avoided if she had eliminated the “with my own hands” part from her wish?” While Madoka had built up enough karmic destiny to grant nearly any wish, her tremendous power as a Magical Girl was also needed to make her wish come true. Causing all witches, including her own, to be killed simply by the force of her wish and allowing Madoka to die upsets the karmic balance of the universe which, as we’ve seen earlier, even Madoka cannot do. In order to accomplish her goal, Madoka needed to use her own power, amplified by the wish, and suffer a consequence equal to the wish she made. All of these points lead to the conclusion that Gen Orobuchi may have found the sole route to a perfect ending for his story, remaining consistent with the rules set up earlier in the show while delivering an unexpected, satisfying conclusion. However there is one potential flaw to Madoka’s wish. If Kyubey and his race are correct, has Madoka’s wish accelerated the death of the universe via entropy?

Now a lot of this is speculation since the specifics of entropy and the energy gathered by the Incubators are never explained. Since the universe is constantly losing energy due to entropy, let’s assume that it can never be permanently stopped. Even if the amount of energy gathered in a single day is enough to maintain the energy density of the universe for a single day (approximately 1.32269872 × 10^54 joules required every second), it means the Magical Girls and Incubators are in a never-ending battle. Now when Madoka becomes a witch in one of Homura’s alternate timelines, Kyubey references no sadness at the loss of earth since Madoka’s transformation gave it nearly enough energy to meet its quota. This raises many unanswered questions. Is earth the only planet being harvested for energy? Can the Incubators somehow store excess energy for future use against entropy, implying that the battle can be won if a certain amount of energy is collected? As said previously, there are few hard facts here so all we can do is hypothesize.

When Homura explains what the pre-wish universe was like, Kyubey immediately mentions that the transforming of Magical Girls into Witches would be a great method of gathering energy since that provides much more power than the Grief Seeds or the Grief Cubes. While we know little about the Wraiths, they seem to be weaker but more numerous than the Witches, each dropping a single black cube (Grief Cube) that contains less energy than the Grief Seeds. Though their greater numbers end up balancing out with the greater power of Witches, Madoka’s universe still lacks the energy that used to be created from the transformation of a Magical Girl into a Witch. If the Incubators aren’t able to gather energy as efficiently, even though its more humane for the Magical Girls, could that lead to a faster universal destruction by entropy?

There are two possible arguments against this claim. Unlike the pre-wish universe where girls often fought each other for control of Grief Seeds, the new universe contains plenty of Wraiths, and consequently Grief Cubes, for them to use. Since there are more opportunities to cleanse Soul Gems, Magical Girls are encouraged to cooperate with each other. While in the previous universe, Magical Girls fighting each other could be of use to Kyubey if it got them closer to becoming Witches, now it serves no purpose. This should lower Magical Girl casualties and make them a more effective force for fighting Wraiths. If they able to defeat tons of Wraiths due to this efficiency, it could compensate for the lack of Witch energy. While this certainly could help, I don’t believe it would be enough to compensate for the loss of the enormous energy created in the Witch transformations.

The other is that if the amount of energy and karmic balance in the pre and post-wish universes are the same, then where does that despair energy go when a Magical Girl reaches the threshold of the good their wish will provide? We see Madoka take the despair of all Magical Girls throughout time in episode 12, but that would suggest that Madoka did in fact change the karmic balance by taking in all that despair. Fans have speculated that more Wraiths are created as a result of Magical Girls reaching their limit. However, this would suggest that evil is still created when Magical Girls are overcome by despair, thus leaving the universe practically unchanged from the pre-wish universe. In order to preserve the power of Madoka’s wish, the universe’s karmic balance needs to be tilted in the favor of good for all despair Madoka took upon herself. However, we established earlier that the karmic balance was one of the universal constants that needs to be maintained. Thus, the accelerated death by entropy is the universe’s way of maintaining the balance despite Madoka taking on all that despair.

Walpurgisnacht is Homura from an alternate timeline, which is why she can't defeat the Witch - as it is herself. Everytime Homura goes to another timeline she makes the Witch more powerful.

While Sayaka falls apart when she learns the truth about Soul Gems, Kyoko takes it in stride and feels sympathetic for Sayaka, trying to stop her from making the same mistake she did. Then you have Mami, who seems like a near perfect magical girl, but when she learns the truth about Witches in one of Homura's alternate timlines, she loses it and begins eliminating all the potential threats to humanity.

The problem is that WN existed before Homura had even become a Magical Girl. In the first timeline, Madoka and presumably Mami die in the process of beating WN. This is what causes Homura to make the contract. Even if we presume that WD is Homura's witch from an alternate timeline, wouldn't that kill Homura and create no more timelines, thus causing the entirety of the series to not occur? Everytime Homura rewinds time, everything that happened in that universe remains there. Madoka's world destroying Witch can't follow Homura trough time, so why can WN.

If you can make an argument on how WN can somehow be the Witch of Homura while Homura is still alive and somehow be able to travel through time, I'd be convinced.