This challenge is for a Persona 5/Puella Magi Madoka Magica, post-Persona 5 and beginning of Puella Magi.

After exiting of juvie and enjoying his last holidays with his friends and comrades, Akira Kurusu, a.k.a. Joker, returns to his native city, that just happens to be Mitakihara, where the recent concentration of witches and magical girls provokes a series of mysterious incidents, such as mass disappearances.

Alongside Morgana, Akira follows a mysterious teen girl (Homura) persecuting a strange white animal (Kyubey) into the first witch's Labyrinth and encounters Madoka and Sayaka and they end surrounded by familiars. Just before they're finished, Akira and Morgana reawaken their Personas and Metaverse appearances and take care of the familiars. Afterwards, Mami Tomoe appears and offers her assistance in defeating the witch and escaping the labyrinth.

Perhaps Homura can save Madoka and everyone in this timeline…

Okay, with some of the plot clear, let's discuss Akira's and the rest of the Phantom Thieves' roles. Obviously, Akira and Morgana will investigate the labyrinths and witches, especially alone. With all their experiences, they're EXTREMELY suspicious of Kyubey, who takes an interest in them.

Just because labyrinths are pseudo-Metaverse Palaces and Witches are the Shadow versions of magical girls, the Phantom Thieves will be able to use their Personas, even in the real world, which will come in handy if they encounter familiars or have confrontations with Homura, who describes them as a completely unknown and unpredictable factor ( with a Trickster with the Wild Card and codenamed Joker, unpredictability is his element).

I think the ability to change from ultimate to initial Personas will come in handy to not appear to overpowering at the beginning and to have a trump card. Oh, in their Metaverse clothes, the Thieves have access to their weapons and physical-enhancing traits of their Personas.

Their relationship with the Madoka cast could vary, from mentor-apprentice like with Madoka for example, or rivalry with the magical girls for any reasons.

For the rest of the Phantom Thieves in Mitakihara, Akira may contact them or they will appear to visit him and Morgana.

There's only one last thing, if Witches are the manifestations of fallen magical girls despair and grief, like said previously, they're like Shadows possessing their host, so why not take a twist?

If a Persona User finishes a Witch, it transforms into a human form Shadow Self in a P4/P5 fashion, which, if convinced to not allow despair to dominate their lifes and try to regain their will to live, the Shadow will return to its hosts unconscious and the corruptive energy will leave their bodies in the form of a Grief Seed, erasing the host's memories of being witches and magical girls (that isn't compulsary, so you can choose if they remember or not) and losing their powers. I don't know about a familiar-born Witch, maybe making them existences like Teddie, for example. That makes them enemies of Kyubey immediately, due to encountering a method to extract a Grief Seed from a Witch and returning them to normal, endangering the system the Incubators imposed for their (in my opinion, ridiculous) long term plans to avoid the thermal death of the universe. Please, if the world is a living being, death will be natural for it, that topic was talked in Persona 3.

Incubators' criticism apart, due to that plothole, Mami will be the one to inflict the coup de grace to the Witch in the first fight, after that, you decide.

If you want more plot twists to the situation, why not add an organization composed of Persona Users and Magical Girls that use the Incubators' system for their own purposes? What is their purpose? And can our heroes dethrone them before is too late? Let's see.

And you can add the Shadow Operatives in the investigation too if you want, having dealt with those situations previously. Heck, you could write a story in that the Incubators implant the Magical Girl-Witch system after the summer holidays of 2009 in Iwatodai Port Island, COMPLETELY unaware of an unnatural hidden hour in which creatures of darkness make their presence known (including the Witches and their Familiars, making it the only time when they can exit their Barriers) and where one of the local high schools is the nest of the majority of said creatures, so the already existent local monster slaying group (obviously SEES) have to solve this situation alongside newbie Magical Girls that they recruit into their ranks. Yes. Everyone with supernatural abilities of any kind can enter the Dark Hour. So expect Mitsuru and the others to have headaches due to being thrown into another paranormal mess. And Persona Users can't be made into Magical Girls after they awaken their potential, unless you want their psyches to be irremediably damaged when they're forcefully relocated into Soul Gems.

Expect to Strega also make profit of the situation in their own manner, after all, what possibilities exist with teenager magical girls that transform into monstruosities filled with despair?

I look forward to see Walpurgisnacht being headshot by Satanael.