There's a possibility that the main antagonist could be an organization. This organization has been secretly researching the energy for their own gain. When they find out that Edward is getting involved, they send their agents to thwart his progress. They might be afraid that Edward will expose their unethical practices related to the energy research.
It could be another alchemist who wants to use this new energy for evil purposes. This alchemist might see Edward as a threat to his plans and constantly try to stop him from learning more about the energy.
Maybe a powerful being from a different dimension who feeds on this energy. This being doesn't want Edward to learn about the energy because if he does, he could find a way to stop it from consuming the energy. So, it tries to create obstacles for Edward throughout his learning journey.
There could be an organization that wants to keep Ki a secret from the world of alchemy. They see Edward's attempts to learn Ki and potentially bridge the gap between the two as a danger. So, the leaders of this organization send their agents to stop Edward, and the most powerful of these agents could be the main antagonist in the fanfiction.
In this fanfiction, the plot could center around Edward trying to understand and control a mysterious new type of energy. He could be on a quest to find the source of this energy. Along the way, he meets new characters, some of whom help him while others try to stop him from achieving his goal of mastering this energy.
Perhaps a new alchemist who is jealous of Edward's skills, even in his new form. This antagonist might see Edward as a girl as an easy target to discredit. They could spread rumors about how Edward's transformation has made him less capable in alchemy, when in fact it's just their way of trying to undermine him.
One possible plot could be that Edward Elric discovers Ki as a new form of energy. He might initially struggle to understand and control it, like he did with alchemy. He could meet a mentor who teaches him the basics of Ki, and then he uses this new knowledge to face his enemies in a different way, perhaps even combining Ki with his alchemy skills.
Edward might meet his parents. Since he has the chance to go back in time, he could meet them when they were alive and perhaps learn more about alchemy from them, which could change his future actions.
It could be someone from within the village who doesn't want Naruto to learn ninshu. Maybe a powerful elder who fears that Naruto will use ninshu to change the traditional ways of the village and undermine their authority.
A powerful and corrupt politician could be the main antagonist. He might be using his influence to cover up illegal activities, and Edward, as an honest cop, stands in his way. The politician could try to frame Edward or have him removed from the case.
A powerful dark wizard could be the main antagonist. This wizard might see Peter's newfound magical abilities as a threat to his own power and plan to either steal Peter's magic or destroy him. He could be someone who has been ruling the magical underworld in New York and doesn't want an upstart like Peter to disrupt his rule.
It could be a character who is jealous of the relationship between Roy and Edward. Maybe someone who wanted to adopt Edward themselves or has a grudge against Roy for taking Edward in.
It could be one of the traditional Volturi members who oppose Edward's presence. They might see him as an outsider who could disrupt their long - established order. For example, Caius might be against Edward joining as he's often portrayed as more rigid and less accepting of new vampires in the Volturi.