Perhaps a new and original antagonist could be created for this fanfiction. This antagonist could be a rogue ninja who has mastered a forbidden jutsu that allows him to manipulate time as well. He could be the one who sets up the events that lead to Minato's endangerment, and Naruto has to figure out his motives and stop him while also saving Minato.
Perhaps an ancient evil that was sealed away long ago is awakened when Minato is revived. This entity could be a powerful demon or a dark ninja from the past. It wants to destroy the ninja world and Minato stands in its way. Minato, with his skills and knowledge, has to figure out how to defeat this ancient evil with the help of Naruto and the other Leaf Village ninjas.
It could be a rogue ninja who is using the poochyena for some sort of evil experiment. Naruto has to stop this ninja from harming the poochyena.
It could be a rogue ninja from Tobirama's time who has a vendetta against the Senju clan. This ninja might have been waiting for the perfect moment to strike at Tobirama when he is alone or vulnerable. Naruto then has to face this powerful and vengeful enemy to save Tobirama.
Maybe an old enemy of Madara who realizes that by targeting Naruto, he can get back at Madara. Since Madara has some sort of connection or interest in saving Naruto in this fanfiction, the enemy thinks that if he can harm Naruto, he can either draw Madara out or simply cause him pain. This enemy could be a powerful rogue ninja with a vendetta against Madara.
It could be someone who wants to take advantage of Minato's new female form. Maybe a villain who has a vendetta against Minato in his original form and sees this as an opportunity to further humiliate or harm him.
Another idea is that Naruto's strong will and determination somehow reach Minato in the past. Minato, inspired by this unseen force which is actually Naruto from the future, finds the strength within himself to overcome a seemingly impossible situation. This could be during the Nine - Tails attack on Konoha, where Naruto's spirit gives Minato the idea to seal the Nine - Tails in a different way that doesn't cost him his life.
It could be someone like Madara Uchiha. He's extremely powerful and his goals are often in conflict with Naruto's. Goku would have to face his Sharingan abilities and his vast array of jutsu.
It could be a new, self - made villain. Maybe a rogue ninja who was once rejected by the Hidden Leaf Village. He blames Naruto for his misfortunes and decides to target his sister as revenge. This villain would have his own set of unique and dangerous jutsu, which Naruto would have to figure out how to counter in order to save his sister.
It could be Palpatine. Since Anakin is going against his wishes by saving the younglings, Palpatine would see this as a threat to his plans. He might send more clone troopers or even some of his dark side minions to stop Anakin.
It could be a rogue ninja from the future who follows them back in time. This ninja might have some vendetta against Minato or Kushina or wants to change the past for his own evil purposes. Maybe he wants to prevent Minato from becoming the Fourth Hokage so that he can take over the village in the future.