Ignoring the whole "abandoned humanity" aspect of the DCEU version of Wonder Woman, I would set it during WW2.
Diana is not a costumed, public "superhero" as Wonder Woman, but she's using her skills to subvert the reign of the Nazis. Paula Von Gunther would be the head of an Ahnenerbe (or similar) institute, an arm of the Nazis which believe that mythological tales, ancient gods, aliens, etc are real. Diana is using her skills and knowledge to track down various mystical / magical artefacts that could be used by the Nazis to give them an advantage during the war. By Diana's side is her friend and archaeologist Barbara Minerva. Diana and Barbara could even be more than friends or in the early stages of opening up their relationship to new levels of intimacy.
On one mission, Diana is in-trouble and, as a last resort, Barbara uses a mystical dagger on herself to become the "Cheetah" to save Diana. But, Barbara is at the mercy of her new "Cheetah" personality and Paula captures the Cheetah to use her as a weapon, both as the "Cheetah" and because she has knowledge about the location of a key mystical / magical weapon (the McGuffin that everyone is searching for). Diana must stop the Nazis while also trying to save her friend.
It could be a little too similar to Indiana Jones or even the first Captain America film, but I think that they could still make the story unique and interesting by focusing first and foremost on the characters. Diana is finally starting to open up again with Barbara after the events of her first film, but her hopes and dreams are stolen with the birth of the Cheetah. And Barbara could be an interesting character in and of herself - finally a chance for a well developed "villain" in a superhero film.
Otherwise, maybe "present day" with Diana researching reports about a cult arising around Circe. Diana and her good friend Barbara discover that it is true and locate Circe to determine what her plans are. Circe forcefully turns Barbara into a were-Cheetah creature to use as her "muscle" against Diana (knowing that Diana is unlikely to use lethal force to stop someone she cares about). Cue some big plan for Circe to become a goddess and replace the old pantheon in order to rule Themyscira (which she views as Paradise because of the absence of men), with the Amazons as her personal army. Wonder Woman saves the day!