It could be a new and powerful dark side user. This character might have emerged from the shadows, having trained in secret, and their sole purpose is to take down Anakin as he is seen as a threat to their plans for galactic domination.
Perhaps a group of bounty hunters could be the ones to kill him. They could be hired by someone who wants Anakin out of the way. The bounty hunters would use their combined skills and resources to track Anakin down and finally eliminate him.
In some fanfictions, it could be an old enemy that Anakin thought he had defeated long ago. This enemy could have been biding their time, gathering strength, and finally gets the chance to take revenge on Anakin by killing him.
It could be the Separatists. They might see Anakin as a valuable hostage to use against the Jedi and the Republic. His skills as a Jedi Knight make him a prime target for them to gain some sort of leverage in the war.
One possible scenario could be that he is killed in a lightsaber duel by a powerful Sith opponent. Maybe this new Sith has some secret technique that Anakin couldn't counter.
The Padawan could be a young alien from a species not often seen in the Jedi order. Maybe an amphibious species that has a different way of sensing the Force due to their unique physiology. This would make for an interesting dynamic as Anakin would have to adapt his teaching methods.
He could interact with Luke Skywalker. Imagine Anakin finally getting to meet his son as an ally in the Rebellion. They could train together and share their knowledge of the Force.
Yoda would be another character. As one of the wisest Jedi, he could sense the strange situation with Anakin and offer his unique perspective. He might be more patient with a child - like Anakin, teaching him important Jedi lessons and trying to ensure that Anakin doesn't go down the same dark path as he did in the original timeline.
It could be his own mother. She might realize that he has become too dangerous and, in a moment of heart - breaking decision, find a way to destroy him. Maybe she discovers a weakness and uses it against him, driven by her love for humanity and the knowledge of the destruction he could cause.
The main antagonist could actually be Anakin's own self - doubt. Since he's in a child's body but has an adult's memories, he might struggle with feelings of inadequacy. This internal struggle could act as an antagonist, preventing him from fully embracing his new situation and using his abilities to the fullest. It could be a psychological battle within himself that holds him back more than any external foe.
It could be about Anakin struggling to connect with his new Padawan at first. Maybe the Padawan has a very different approach to the Force than Anakin does. For example, if the Padawan is more in tune with the peaceful aspects of the Force while Anakin is used to a more aggressive style. This difference could lead to some initial clashes between them. But as they go on adventures together, they gradually learn from each other and form a strong bond.
In some fanfics, it could be Anakin's own self - destructive tendencies. He has made so many bad choices in his life that in the end, his own actions lead to his death. For example, if he continues to pursue the dark side without fully understanding its consequences, it could ultimately consume him and lead to his demise.
Anakin's mother, Shmi, would likely be a very important character. Since Anakin is not being trained as a Jedi, he would be more focused on his family. Shmi's influence on Anakin would be even greater, and she could play a role in guiding his actions and decisions, especially in relation to the local community on Tatooine.