In a time - travel story, it could be an alternate version of Ezra himself. Maybe Ezra from a different timeline where he turned to the dark side. This dark Ezra would oppose the normal Ezra, seeing his attempts to change things as a threat to his own power and the dark future he has created.
Perhaps in the fanfiction, the Empire discovers a connection between Ezra and Revan and tries to use it against them. They create a false prophecy that says Ezra will become like Revan and bring destruction. Ezra has to prove that he is different and that he will use Revan's story as a guide to bring peace and justice, not chaos.
A new, unknown dark side entity could be the main antagonist. Maybe Revan's time travel creates a rift in the Force that awakens a powerful being that feeds on chaos and destruction. This being would oppose Revan because his actions of trying to fix the timeline would go against the chaos that the entity thrives on.
Well, in a lot of Star Wars Rebels fanfic, Ezra being sick often serves as a catalyst for emotional moments. The other characters like Kanan or Sabine would be worried about him. It can also create some interesting dynamics within the group. Some might be overly protective, while others could be more focused on the mission but still concerned. And it might be a chance for Ezra to grow in his understanding of his friends' care for him while he's in a weakened state.
Well, that's a matter of personal opinion. Just because someone might think Ezra is stupid in fanfiction doesn't mean it's a universal view. In the official Star Wars Rebels story, Ezra has his own growth and development. However, in some fanfictions, the author might be trying to explore different aspects of his character or create unique storylines that could make him seem less intelligent, but it doesn't represent the whole view of Ezra's character.
Ezra being 12 in the fanfiction could lead to plots centered around his coming of age and facing challenges with a younger mindset. Maybe he has to prove himself despite his age.
Hera could also be an interesting character to pair with Ezra. She could act as a mentor figure in a fanfiction, guiding Ezra through some tough decisions regarding the Rebellion. Their relationship could be explored more deeply, especially in terms of Ezra learning from Hera's leadership skills.
It could be a slaver boss. This character might be someone who has a network of slaves and sees the Seventh Sister as a valuable asset. He is cruel and only interested in profit. He would constantly try to break her spirit and force her to do his bidding. Maybe he also has some knowledge of the Force that he uses to keep her in check. Also, it could be an alien warlord who enslaves the Seventh Sister to fight in his gladiatorial arenas, seeing her as a great addition to his entertainment.
He could be kidnapped by a group of pirates who mistake him for someone else. These pirates are known for their ruthlessness. The rebels would need to negotiate with other pirate groups to get information about Ezra's whereabouts. It would be a story full of danger and unexpected alliances.
The plot could be that Ezra loses his lightsaber in a skirmish with the Empire. He then embarks on a dangerous mission to retrieve it from an Imperial stronghold. Along the way, he teams up with some unlikely allies who help him infiltrate the base and get his lightsaber back.
Meeting a powerful dark side entity that can manipulate their minds. This entity could make them see their worst nightmares as if they were real. For Kanan, it might be the fall of all his friends and the destruction of the Rebellion. For Ezra, it could be the death of his family all over again. They have to fight against this mental intrusion and their own fear.