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This is a "Wild Mass Guess" entry, where we pull out all the sanity stops on theorizing. The regular entry on this topic is elsewhere. Please see this programme note.
To the Stars
Ryouko is destined to become a cosmic entity not unlike Madoka.
That wish of hers to "find her place in the universe" is going to go horribly right.

Ryouko's magical girl outfit is specifically intended to look like Madoka's.
Not her goddess outfit, but Madoka's original pink and white uniform. Maybe the author wants them to look alike for thematic reasons. Maybe there's an in-universe justification for it, like Ryouko is descended from Madoka's brother or something. But don't all these features sound familiar?
  • Lacy dress goes from chest to calves.
  • Flares out and ruffles at the bottom.
  • Sleeves flare out and ruffle.
  • Buttons on the chest.
  • Soul gem at the base of her neck, on the front.
  • Weapon that shoots arrows.
The magical girl in purple from chapter 5 also has buttons, a lacy dress, a soul gem at the base of her neck, and a bow. If the similarity between Ryouko and Madoka is intentional, then whatever is causing it probably applies to this girl as well.
  • Confirmed - Hieronym's tumblr for the fanfic reveals that Ryoko's outfit is very similar to Madoka's. Whether or not there is any thematic significance to this is still up in the air.
    • Word of God is that costumes probably follow through bloodlines and that Nana and Nakase's uniform design is most influenced by their still unnamed mother's family. This, along with Hieronym's insistence to keep in mind that sometimes the paternal family has more influence on costumes, seems to imply that Ryouko could also be somehow related to Madoka and descended from Tatsuya's line.

Also, Ryouko mentions in chapter 9, during her vision, that the Goddess looks familiar. Perhaps regular Madoka is familiar to her as well, and Ryouko is subconsciously mimicking her? Or perhaps any similarity to Madoka is a coincidence and Ryouko only resembles the purple magical girl, due to hero worship or a family connection or something.
  • Not exactly. Ryouko is descended from Hitomi, but from an estranged branch of the family tree.
    • That's a bit hasty. Ryouko is already known to be a descendant of both the Kuroi and Shizuki families. Another ancestor from the Kaname line remains a distinct possibility.
  • Confirmed as of Chapter 32 : Ryouko is Tatsuya Kaname's great-great-granddaughter, and thus Madoka's great-great-grandniece

Ryouko is the indirect descendent of either Sayaka or Madoka.
In the second chapter, Mami notes that when she saw Ryouko the system should have flagged the relationship she has to someone from far in the past. Mami felt relief that the computer didn't know things from so far back and that "she had found herself looking at a face she hadn't seen in a long, long time.". This would indicate someone from the original show.

Hitomi or Kyosuke's descendents wouldn't flag high on Mami's radar and while Ryouko has the same last name as Hitomi any of Hitomi's children would have the father's last name, Kyouko's still around, and Homura disappeared without descendents. If she had any, the Cult of Hope would have incorporated their entire line into the church already. This leaves Sayaka, who may have cousins or the like or her parents had another child, or Madoka, who Mami does not know but who did have a living brother. Homura may have mentioned Madoka's family at one point and dragged Mami and Kyouko to see them on occasion.

The mention in-fic about the ability to become a magical girl running in families also helps to support this idea. The aching feeling of familiarity Ryouko felt could have either been a feeling all magical girls have for Madoka or the feeling of meeting a long-lost relative who was dearly close before vanishing.
  • Close, but not quite. As noted in the previous WMG, Ryouko is descended from Hitomi.
    • Hold on there. That Ryouko is descended from the Kuroi and Shizuki families does not rule out a Kaname ancestor as well.
In chapter 15, Homura says that she knew Ryouko's maternal grandmother's grandfather. Given that she was still trying to keep his dying wish so much later, she was probably close to him. Homura isn't exactly the type to go befriend random people, so this man may well have been Madoka's little brother. Suspiciously, at this point we know the names of all of Ryouko's grandparents except for her maternal grandmother.
  • Confirmed in Chapter 32 : Ryouko is a descendant of Tatsuya Kaname, Madoka's little brother and acquaintance of Homura.

Hitomi became a magical girl and had children, making her the ancestor of Ryouko.
In the opposite direction of my other guess, Hitomi is Ryouko's ancestor. Nearly as old as the others, it would be a surprise to anyone that she's still kicking at her age. Having previously been Madoka's friend and having a similar personality as her, it wouldn't be too much of a surprise for them to have similar powers and outfits. Their previous connection would make her a good person for Madoka to use for manipulating their plane.
  • So close! But not really. The story implies that Hitomi herself doesn't contract. But her daughter Sayaka did. Indeed, she appears in Chapter 14 as one of the Ancients, who also happens to be the matriarch of Ryouko's father's side of the family tree.

Simona is a Honey Trap sent by the Black Hearts to recruit Ryouko.
Why? Because of Ryouko's parents. She intentionally finds potential magical girls who need a push and who are very likely to be powerful. By getting close to them and exposing them to demons, potentially powerful but purposely sheltered magical girls can be awakened and entered into the corps away from interfering forces, this one being Ryouko's parents. Simona goes from place to place to fulfill her role and recruit as many girls as possible.

The missing magical girls are being used as guinea pigs in a misguided attempt to learn how to prevent girls from dying of corruption.
If you don't believe Homura and Kyouko, then you would probably think that disappearing after soul gem corruption is a natural magical process without any guiding intelligence. But Homura seems to provide evidence that soul gem corruption doesn't need to be fatal. And truthfully, it shouldn't be. Perhaps anyone with a sufficient understanding of magic could realize that girls whose soul gems are blackened don't need to disappear to another plane. Clearly, the next step is to research how to extend Homura's case to everyone. If technology can stop aging, the natural death of all humans, why not stop corruption, the natural death of all magical girls? Of course, Homura is the only one for whom living with such great soul gem corruption doesn't mean a fall into despair and the birth of a new witch. So to the frustration and befuddlement of those who don't believe, every attempt to extend the lifespan of girls with black soul gems would end in their mysterious disappearance (into Madoka's arms). But surely they're on the verge of getting it!

This explains why Madoka is getting personally involved. Her wish has helped behind the scenes, but this affront to her nature needs direct intervention. Resolving it requires someone who believes in her and can understand why forcing girls to stay alive with corrupt soul gems is a bad idea. Poison Oak Epileptic Trees bonus: Yuma is involved in this but is keeping it a secret because she knows Kyouko would flip shit.

Super-saturated grief cubes are created by causing massive excess soul gem corruption and dumping it on the cubes.
It's fast, it's morally questionable, and one magical girl working alone can do it without having many more grief cubes than she would normally require. It could explain where the missing magical girls are and what the Southern Group's "research" was.
  • Rereading Ch. 8 (Kyouko and Yuma's conversation), it seems pretty likely that Oriko discovered some kind of method to create super-saturated grief cubes, which create especially powerful and/or numerous demons if something goes wrong (or right, depending on what you're using them for) - Yuma specifically asks whether the group that attacked Ryouko and Simona was 'unusually hard to fight'. This explains why Oriko's group was unexpectedly wiped out by a horde of demons they (according to Mami) really should have been able to handle. Their habit of going after more emotionally unstable girls from other teams also fits with the above theory - go after them, induce corruption on the more vulnerable member in some way, use grief cube to store for later use. (The other method of summoning a similarly massive horde apparently involves stockpiling grief cubes for about a decade, and was likely impossible before the MSY's teamwork created a surplus.)
  • An alternative theory : the Incubators found a way to create super-saturated Grief Cubes, and used them to get rid of the Southern Group. After all, they dispose of all the fulled Grief Cubes, so dumping massive excess of corruption in some of them or stocking a small amount of them during a decade or more for an occasion where they need to more directly intervene shouldn't be too difficult for them.

Researchers are trying to weaponize demons.
It would be really great if they could airdrop/teleport some super-saturated grief cubes in and then run away laughing. But who knows if demons would even notice the aliens.

Oriko has an evil-but-necessary plan.
Oriko is still alive. She foresaw the alien attack and has been preparing for a long, long time. Through experimentation and manipulation on a colony, she's created a method of dealing with cephalopods that is effective but morally appalling. It's so appalling, in fact, that at least some factions in the MSY try to shut it down. Ryouko's vision of Kyouko dying was part of that attempt.

The Incubators are behind the alien invasion.
A consequence of the MSY is that magical girls are now sitting on entire storehouses of Grief Cubes, which are only useful to the Incubators once full of corruption from the soul gems. Except that with the advance in technology brought by the MSY, Earth is a near-utopia and it's probable that the colonies will follow suit, which will generate less grief and negative emotions from mankind, and with it less Wraiths and less filled Grief Cubes. So what better way to make grief massively generated by mankind and the Magical Girls to use their massive stockpile of Grief Cubes than a war? The cephalopods are actually under the Incubator's orders, and where sent to attack humanity in a war of extermination, but which strangely relied on Hollywood tactics and showing off, with their full scale and serious assaults always only barely lacking the punch necessary for a total victory. As a bonus, the MSY had to reveal the existence of MG to save mankind, which combined with the war effort would push much more girls to contract, with all the extra Grief Cube consumption that comes with it.

Or even worse : maybe the alien invasion was always a part of the Incubator's standard process of harvesting energy : once the targeted civilization reaches a technological threshold where it could survive an alien invasion, they start the "intensive cultivation" phase of their plan by putting the civilization in an inescapable war for survival until the Incubators reach their energy quota.

Expanding on the above, Oriko foresaw the invasion and the Incubators' role in it.
Oriko saw the true colors of the Incubators, how their quest for more energy would lead them to trap humanity in a massive war for survival once the technological advance would let them survive against the cephalopods, just so they could fulfill their energy quota for Earth. We already saw it in the pre-Madoka universe, where Kyubey forced Madoka into contracting in many of Homura's failed timelines while knowing that she would become a world-ending Witch, but not caring the least because that would let him reach Earth's quota. And Oriko also saw a way to survive against the cephalopods : by uniting all the Magical Girls into one powerful organization, powerful and organized enough to create a stable system for the MG where there aren't any needs of infightings for Grief Cubes, and which will be able to mobilize all the MG of humanity to fight back and win against the cephalopods, and maybe in the long term unmask the Incubators' treachery and be freed from their schemes.

Everything she did with the Southern Group was geared toward the objective of founding a MSY as strong and organized as possible in the mother of all Genghis Gambit : they trashed Mami's apartment to goad her into directly attacking them in a place that was withing Kyouko's reach, inciting her to help Mami and rekindle their friendship (and keep in mind that Oriko can see the future, so she would had know that Kyouko would go help Mami), and attacked various MG groups to give them a common enemy which later incited them into uniting into what would later become the MSY. Even the apparent random slaughter of magical girls could be explained as Oriko trying to kill the more unstable elements of every groups who would later go mad and threaten the unity of the alliance (their teammate would rather try to protect their sisters-in-arms rather than submit to a still new magical girl coalition). Even after the Southern Group destruction, their actions heavily influenced the MSY charter and the creation of the Soul Guard (and later the MHD) to take care of the criminals and insane magical girls, ensuring the security and stability of the MSY, especially in times of war.

That's why the Incubators were so cooperative with the other groups in the conflict against the Southern Group, breaking their usual absolute neutrality, (remember that they keep their neutrality even in a war for survival against aliens of incomprehensible advanced technology!) : they somehow discovered what Oriko foresaw, and want her dead before she can throw a spanner in their plans. They are also behind the mysterious disappearance of the precognitive class of magical girls and total absence of new ones contracted since then : they managed to have the remaining precogs hunted down, and didn't contracted with girls who could become precogs, or somehow found a way to prevent a magical girl to become one upon contracting, "vetoing" that power when their contract is made. All of this so no other magical girls would discover the truth.

For bonus points : Oriko put Yuma into the confidence of her vision and true motive, she foresaw the potential Yuma had and the vital part her skills would play in the MSY, and entrusted her with continuing her work on assuring the MSY's strength and stability. That would explain why she took Yuma under her wings, even though her profile was very different from the typical Southern Group member. Oriko's cadaver moving and directly looking at Ryouko during her vision of the Goddess in chapter 9 could mean two things :

- Oriko is still alive, continuing her secret fight against the Incubators, and managed to stay under detection thanks to Yuma's control over the government's surveillance systems.

- she died, but it symbolize her plan continuing long after her death via Yuma and all the butterfly effects she set in motion with her precognition powers.

The cephalopods came to be in their current state due to an alien's wish.
For some reason, in twenty years no one has made a wish to end the war. Could the aliens be somehow shielded from magical influence? The cephalopods have never demonstrated magical capabilities, but that doesn't mean they never had them, or that they never interacted with another species that had them. Especially implausible and unsubstantiated addendum time: maybe the cephalopods, or some subset of them, banished the Incubators and/or destroyed their own magical potential in the old universe, before Madoka made things better. For whatever reason, Madoka's wish left the world with mostly the same history, so that wish couldn't be undone since it would have too large of an effect.

Homura will be revealed to have been captured and forced to reveal the truth by a faction working to undo Madoka's efforts and return the magical girl system to before madoka changed it.
Magical girls since Madoka changed everything do not know that originally they didn't have to fight demons but their own kind changed into monsters after falling into despair and that is why Sayaka Miki is barely talked about by those from that time who knew her because surely the last thing they want to say is that "oh by the way Sayaka is really gone because she was a heartbroken idiot who self-serving wish led her to fall into despair and we had to put her down because she transformed into a monster that would had tryed to kill us all."
  • But Sayaka didn't turn into a Witch. At the end of episode 12, Madoka vanishes her when her Soul Gem is corrupted. She's not talked about because, unlike the other members of the Four, not much is really known about her and she died before the Four did any of their famous actions (fighting the Southern Group, founding the MSY, the battle of New Athens, etc.)
  • While the premise of this guess is incorrect, the guess itself is actually still possible. Homura being involved in an attempt to undo Madoka's wish is possible, because she's the only individual that remembers the Witches in the first place. Whether she would do so against her will is another matter, because it's hard to imagine anyone overpowering Homura, and if Madoka's Wish is undone, they might be able to see each other again.

Simona Del Mago is Homura.

Ryouko was genetically engineered.
Between Asaka's remarks in Chapter 9, as Ryouko was getting fitted with implants:
“Her genetic profile is outside the five-sigma safe limit for using the customary procedure,” Patricia said airily, clearly not quite focusing on the conversation. "About six, to be more precise. Can't really get greater precision so far out."
Ryouko's vision of being inside a tank of fluid in the same chapter:
"she was screaming, and she was looking up at the impassive eyes of two men, immensely large, wearing the universal blue of hospital staff. They looked distorted, almost as if she were looking at them through glass.
She raised her hand, and it was wet. She was in some sort of fluid, and when she pressed her hand forward, she contacted glass. It really was glass, or perhaps plastic. She was in some sort of tank. And her hand seemed strangely shaped, and difficult to move."
and the exchange between Ryouko's father and his colleague in Chapter 13, as they prepared to upgrade Ryouko's TacComp:
“Unusual genetics in her file,” one of the technicians commented, shaking a vial. “Your daughter is unique, Kuma-san. It just means more work for us.”
It was said in the vein of a joke, and her father, who apparently knew the man, smiled and nodded, catching the intended humor.
Not getting the reaction he had been expecting—namely, a question about the unusual genetics—the technician was briefly awkward, then turned back to his work.
Ryouko watched the exchange, a little puzzled.
and Goddess Madoka's enigmatic remark in Chapter 29:
“But, it is easy to manipulate history, if you know how,” the girl said. “Even if you have very little direct influence. A suggestion here, a vision there, a well-timed demon spawn—you don’t know it, but this is one of the things you were born for. Your wish made sure of it.”
the reader might suspect that there's something special about the circumstances of Ryouko's birth, beyond what we already know. Plus, we know her parents are biological researchers, responsible for developing the secretive magical girl cloning project.

Expanding on the above, Ryouko is a Human/Ceph Hybrid
As part of her conception process, she was spliced with alien DNA, maybe to make her a super soldier able to use their superadvanced technology. There are various elements that could point toward a Ceph influence :

  • her disturbing Blood Knight tendencies - Kyouko even commenting, just after Ryouko's first fight against Wraiths, that she never saw a just-contracted girl exhibiting battlelust before - culminating into a fit of crazed blood lust in chapter 26 when she charges and punches to death an alien sniper in retaliation for the death of her teammate. Besides, Ryouko states that when in one of those episodes of extreme Blood Lust, she feels a sense of complete certainty and concentration that is completely at odds with her usual personality. She also shows at various occasions a fascination for blood and injuries, such as when she examined her grandfather's bloody leg stumps, or after the above beating of an alien sniper to death where she had to fight back the fascination she was feeling at what she did.

  • her teleportation power works over displacing matter like a wormhole, which is a trademark technology of the aliens.

  • it's mentioned in chapter 26 that the green of Ryouko's Magical Girl uniform is exactly the same than the aliens' blood.

  • finally, the author posted a link to the real life genetic anomaly knows a "chimerism", explaining that it's relevant to the last chapters, heavily implying that one of the characters is a "chimera".

If the Cephs' complete ruthlessness and lack of doubts in exterminating mankind and extreme brutality are "hardcoded" in them via Genetic Memory, and also benefit from innate knowledge such as wormhole/black hole-based technology, it would explain Ryouko's unique powers and violent tendencies.

For bonus points, Ryouko shares a name with another female main character who's revealed to be an half-human hybrid!
To Kill A ThiefWMG/Fan FicTurnabout Storm

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