Perhaps a powerful criminal organization. If Joe is representing a witness against them, they would stop at nothing to intimidate the witness and make Joe drop the case, using threats, blackmail, and other dirty tactics.
A rival law firm could be the antagonists. They might try to steal Joe's clients or undermine his cases in unethical ways, like spreading false rumors about his legal abilities.
A group of rogue ninjas who have made the island their base could be antagonists. They might see Naruto as a threat to their operations on the island.
A powerful wizard who wants to use the 'lady of darkness' powers for his own evil gains could be an antagonist. He might try to manipulate her into doing his bidding.
The Death Eaters could be antagonists. Even though Regulus turned against them, they might not forgive his betrayal and try to harm him or the school where he teaches. They could send spies or launch attacks to get revenge.
The other Death Eaters could be antagonists. They might not trust Snape completely and try to undermine him. For example, Bellatrix Lestrange could suspect Snape's loyalty to Voldemort and try to expose him while he's alone, which would put him in a very dangerous situation.
Some of the remaining members of the Akatsuki who still hold grudges against Sasuke or see the baby as a threat to their plans. They might target the baby to get revenge on Sasuke or to use it as a bargaining chip. For example, if there are any Akatsuki members who were loyal to Itachi and don't like Sasuke's new life with Naruko, they could cause trouble for the family.
A group of traditionalists in Akeno's world could be antagonists. They might not approve of the idea of a harem or of an outsider like Naruto having so much influence. So they could try to break up the harem and drive Naruto out of their world by using political means, like spreading false rumors about Naruto and his friends.
In Percy Jackson father fanfiction, the sea god Triton could be an antagonist. He might be jealous of Percy getting so much attention from Poseidon. The primordial sea gods or goddesses could also be antagonists. They might see Poseidon's relationship with a half - blood as a perversion of the natural order. And then there are always the minor gods who might feel that Percy and Poseidon are getting too much power and try to undermine them.
There could be a dark spirit that haunts the woods. It's jealous of Bella's presence and tries to drive her out. Another antagonist could be a neighboring landowner who wants to expand their property into the woods where Bella lives.
If it's a crossover with the One Piece world, Blackbeard could be a potential bad guy. His ability to steal Devil Fruit powers and his ambition to become Pirate King could lead to a clash with Gohan. Gohan's pure - hearted nature would be in opposition to Blackbeard's more devious ways, and their battle could be epic, with Gohan's ki powers against Blackbeard's dark powers.
Perhaps a powerful and corrupt merchant group could be the antagonists. They are secretly trying to take over the village's economy and resources. They use bribes and blackmail to get their way. The Sixth Hokage discovers their plot and has to stop them without causing too much chaos in the village's economic system. They may also have some ninja mercenaries working for them.