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Here are things we haven't found out yet.

This is not a complete list.

  1. Why did Simona del Mago put the wrong names for her parents on her school transfer papers? Chapter 53
  2. Why was Simona staring at Ryouko on her first day of school in Mitakihara? Chapter 56
  3. Who dropped supersaturated grief cubes in the park in Chapter 1? Why? Chapter ?? (Recent)
  4. Why are magical girls reporting missing grief cube shipments in Cult surveys?
  5. Why are magical girls reporting missing colleagues in Cult surveys?
  6. What bothered Patricia after Ryouko got her implants upgraded in Chapter 9? Chapter 34
  7. Why does Ryouko's soul gem glow in the presence of active FTL technology? Chapter 29
  8. Where is Homura?</s? Chapter ?? (Recent)
    1. Partially answered, but now she's gone again.
  9. Why did the Cephalopods attack? What is their goal? Why are they continuing to fight a war for which they were unprepared? Chapter 65
  10. Why has nobody wished away the war?
  11. Why did the Cephalopods raid Ryouko's transport in Chapter 20?
  12. What was the nature of Joanne Valentin's "religious experience"? Chapter 58
    1. Is Joanne Valentin telling the truth about who she is? If not, who is she?
  13. Why would Kyouko be a target for foul play during an amphibious assault on a Core World the raid on X-25?
  14. Why are there no more precognitive magical girls?
  15. Why can Ryouko's TacComp perceive her Ribbon experiences? Is Clarisse the only TacComp v2 that can do this, or can they all do it? What does this imply about Clarisse's relationship with her host? Chapter 45
  16. How much of the future history been influenced by the Incubators? The MSY? The effects of wishes?
  17. What is the nature and purpose of Ryouko's chimeric DNA? (Recent Interlude)
  18. Who is responsible for Ryouko's genetic modifications? Chapter 58
  19. What happened between Oriko and Yuma 450 years ago just before the former's death? Is she really dead? Chapter 44
  20. Who subverted the TCF? Why?
  21. What, exactly, was Homura's wish? We have a clue from the Akemi movie, but Kyouko hints that it's not quite right...
  22. Emotions are not a suprise to the Thinkers (despite not usually having them) and Feathered‐Defender has emotions. Why then aren't there any species capable of contracts amongst the Concensus?