I don't want to elaborate much but here is what I think will happen in the third movie:
Spoiler for Long bunch of speculation...:
-Begins with Sayaka's heroic sacrifice.
-Homura has nightmares about Madoka being defeated by a monster and everything sinking into the darkness.
-Witches will return as half-mutated ax crazy magical girls.
-Oriko will help Homura find the source of them, she predicts a white haired demon will rip the goddess from heavens and throw magical girls into hell.
-A new magical girl will join the group and later betray everyone to be revealed as the main villain.
-She is a Kyubey girl goddess.
-The world will end by her doing and the movie will flash foward to a war between demons, witches and magical girls.
-When everything seems lost and Homura is about to die, Madoka will finally intervenes.
-Major battle between Madoka and the Kyubey goddess.
-Kyubey goddess transforms into a massive demonic monster the bigger than Earth, cue space battle with giant Madoka.
-Madoka is on the verge of defeat when Homura determination gives her the power to injure the demon and allows Madoka to turn the tides and win.
-The duo is cheering up their victory with Madoka stating that she will restore Earth and revive everyone but she is gruesomely impaled by a Spear of Longinus.
-Homura despairs before the seemingly dead Madoka and the prospect of being left alone and unable to turn back time.
-Enters the bigger bad and offers her the power to save Madoka by revealing that the latter was an eldritch abomination stuck trying to save corrupt magical girls who only made chaos in Madoka's "heaven" because they refused to move foward.
-Homura finally breaks down entirely, considering those relying on Madoka and dragging her down as parasites so she wishes to release Madoka from the burden of fighting for those who can't be saved.
-Homura's hair turns white as she begins turning into a goddess of darkness and detroying all soul gems through time and space and plunging them into a torrent of despair.
-Madoka revives and stops Homura before is too late, the later faints.
-Big bad reveals that the purpose of the magical system is to make souls reject evil and find paradise in their hearts.
-The Kyubey girl, who is alive but unconscious, was the previous goddess who made the witch system because in her universe people consumed all energy and destroyed everything.
-Madoka was destined to became a saviour goddess because the previous system was flawed and too harsh but her own was too kind and indulgent turning magical girls into selfish ignorant fools.
-Homura was destined to balance Madoka's salvation because their souls complement each other and the former can take tough actions Madoka cannot bring herself to do.
-Universe resets with Sayaka alive and hooked up with Kyoko as their new group fight a shadow battle against witches, corrupt magical girls who refused salvation and feed on human despair to live, and demons, familiars of witches who gather despair to prolongate their master's lifespan.
-Mami is a witch hooked up witch Charlotte.
-Madoka and Homura are together on weird terms and everybody gainaxed ever after.