Speculah:Homura Identity Swap Theory
The following speculah was generated by students at a school in Germany:
The character currently known as Homura was actually a Puella Magi who was killed before the beginning of the story proper. Her Soul Gem was still intact following her death, and took control of the body of another girl -- either because the girl in question incidentally picked up the Gem, or had been recently killed by a witch. Kyubey was not aware of the body swap, and refers to Homura as an Irregular because he doesn't recognize her as one of his contractees. Through her own experiences, Homura came to realize that Soul Gems function as phylacteries, and understood that retrieving Sayaka's Gem from the truck would save her life.
"Akemi Homura" is probably the name of the host body -- by chance sharing a given name with the Puella Magi that currently inhabits it. Homura dislikes the name "Akemi" because it reminds her of the soul she displaced. (Compare with Speculah:Names). It is possible that Homura's "original self" knew Madoka.
After Sayaka's transformation into a witch, her body was left abandoned but uninjured. Homura might be able to take control of it, allowing her to use both bodies at once while fighting Walpurgis Night. She could also take Sayaka's place in normal society to defuse the suspicion that would be aroused by Sayaka's death and to enjoy a happy school life with Madoka. Alternatively, Homura could use Sayaka's body to travel back through time and attempt to change fate again if she's defeated in the fight against Walpurgis Night.
In Puella Magi Kazumi Magica, the Pleiades Saints encounter a Puella Magi known as Ayase Souju. Ayase, who collects Soul Gems, shares her body with another Puella Magi named Luca. As such, she can use two sets of magical abilities, and continue fighting even if one Soul Gem is stolen or broken.