In this fanfiction, it could be that Dr Strange himself becomes an antagonist in a sense. The power he used to survive the snap has some unforeseen consequences. It starts to corrupt him and he begins to think that he should be the one in control of the new universe. His actions then put him at odds with the remaining heroes who want to restore the old universe. They have to find a way to stop him from causing more harm while also dealing with the aftermath of the snap.
Thanos could still be the main antagonist. Just because Dr Strange survived doesn't mean Thanos is defeated. He might be on a quest to find out why Dr Strange survived and finish the job. Also, there could be other villains who emerge in the power vacuum left by the snap, and they could team up with Thanos or work against both Thanos and Dr Strange.
One possible plot could be that Dr Strange uses his magic in a way that shields him from the snap's effects. Maybe he creates a temporal or dimensional bubble around himself just in time. He then has to figure out how to reverse the snap while dealing with the chaos that ensued. He might travel through different dimensions to find a solution or seek help from other powerful entities.
Thanos could be an interesting antagonist in a crossover. Imagine Dr Fate having to use his magic to try and stop Thanos from getting all the Infinity Stones. Thanos' brute force and determination would be a great contrast to Dr Fate's magical finesse.
Obviously, Spider - Man (Peter) himself. And perhaps Aunt May, who would be very relieved that he survived but also worried about the state of the world. Ned could also be there, being Peter's best friend and all. They could be trying to figure out what to do together.
The Akatsuki would still likely be the main antagonists. They have their own goals that often conflict with the well - being of the ninja world. Even with Minato alive, they are a powerful and organized group that would pose a great threat.
Doctor Strange is the main character. And the Ancient One also plays a very important role.
It could be a powerful sorcerer who has turned to the dark side. This sorcerer might be using his magic to manipulate events in Sherlock's world for his own gain. He could be creating illusions and false trails to throw Sherlock off, while also using his magic to fight against Doctor Strange.
It could be someone from the Naruto universe who doesn't like Naruto's newfound fascination with Aku. For example, Danzo might see Naruto's interest in Aku as a threat to the stability of the village and try to stop Naruto from further exploring Aku - related things. So, Danzo could be the main antagonist in this case.
Maybe in the fanfiction, Peter survives the snap but his powers are affected in some strange way. He has to figure out how to control his new - or rather, altered - powers while also coping with a world that has been turned upside down. This could involve him teaming up with some unexpected allies.
Dr Strange himself is the main character. He's a brilliant neurosurgeon turned sorcerer.
Well, in one comic arc, Dr Strange was killed by Mephisto, who exploited a weakness in his magical defenses.