Perhaps the main antagonist could be a powerful and corrupt wizard from the Ministry of Magic. This wizard might see Harry as a threat even though he has left magic behind. The wizard could be afraid that Harry might one day return and expose his misdeeds. So he tries to eliminate Harry in the Muggle world, using both magical and non - magical means to achieve his goal.
It could be a new dark wizard who rises to power in the wizarding world. This wizard blames Harry for leaving and believes that his departure has made the wizarding world weaker. So the new dark wizard sends his minions to the Muggle world to force Harry to return to the wizarding world and face him, or else he will start causing chaos among Muggles which Harry has come to care about.
In a 'Harry Potter left magic behind' fanfiction, the plot could involve Harry feeling guilty about all the destruction magic has caused. So he abandons it and starts anew in a remote place. He tries to build relationships with Muggles based on honesty. But as time passes, he realizes that magic is a part of him and he has to find a balance. Maybe he starts teaching some Muggles about the good side of magic in a very discreet way to help them better understand the world around them.
Maybe the main antagonist is an ancient magical being that has been awakened by the disturbance caused by Harry's exploration of the 'Mind of Magic'. This being believes that the wizarding world has strayed from the true path of magic and sees Harry as a symbol of this deviation. So, it decides to target Harry and try to bring back what it considers the 'pure' form of magic, even if it means destroying the current wizarding society.
In some cases, the antagonist could be a group of magical creatures that have been wronged by wizards in the past. They see Hermione as a representative of the wizarding world and when she is left behind, they try to make her pay for the past wrongs. These creatures could have unique powers and abilities that make them a formidable foe for Hermione.
It could be a powerful ninja from another village who sees Naruto's godlike powers as a threat to his own plans of domination. Since Naruto is already feeling vulnerable due to his family leaving him, this antagonist might try to take advantage of his emotional state.
Perhaps a long - lost relative of the Potter family who feels they were unjustly excluded from inheriting the manor. This relative could be jealous of Harry's status and the wealth associated with the manor. They might use dark magic to try and claim what they think is rightfully theirs, leading to a battle of magic and loyalty within the Potter family and among Harry's friends.
It could be Malfoy. He might make fun of Harry for wearing a dress and try to use it to humiliate him in front of the whole school, which would then lead to a conflict between them that goes beyond the usual rivalry.
Perhaps a new dark wizard or witch who has infiltrated the Ministry of Magic and made sure Harry was sent to Azkaban. This antagonist could be working towards a bigger plan to take over the wizarding world and sees Harry as a major threat even when he's locked up.
Maybe a dark wizard who has an interest in Harry's newfound inheritance. This antagonist could want to steal his powers or use him for their own evil purposes. They might see Harry as a key to unlocking some ancient and powerful magic that they've been seeking.
Perhaps a group of dark wizards who think that by disrupting time, they can bring back the dark ages of wizardry. They target the Timekeeper as the only one who can stop them. They use dark spells and curses to try and stop the Timekeeper from fixing the time - related problems they create.
It could be Voldemort. He might see Harry's new waterbending ability as a threat and try to find a way to counter it. Maybe he would seek out dark magic related to fire to oppose Harry's water powers.