It could be a power - hungry scientist who wants to use April's world for his own experiments. He might see the unique elements of the world as a way to gain ultimate knowledge and control.
A long - lost relative of April's could also be the main antagonist. This relative has a grudge against April's family for some past event. They come back to the world with a plan to take revenge and in the process, they cause chaos and destruction. This antagonist would have a personal connection to April, which would make the conflict more intense and emotional.
Perhaps a group of rebels who oppose the current order in April's world. They believe that April and her allies are the ones causing problems and they try to disrupt the peace. Their motives could be based on a misunderstanding or a different view of how the world should be run.
I'm not entirely sure, but I assume April is one of the main characters since the title has her name in it.
Madara Uchiha is another obvious candidate. Even though he was defeated in the original story, in a fanfic he could be resurrected with even greater power. His Sharingan abilities and his knowledge of the ninja world's secrets would make him a formidable antagonist for taking over the Naruto world. He could manipulate different clans and villages against each other before making his move to take over.
Perhaps a group of anti - technology extremists could be the main antagonists in an Ultron fanfic. They see Ultron as the symbol of all that is wrong with technology and are determined to take him down, no matter the cost. They might use their own advanced, but more rudimentary, technology to fight against Ultron. This would create an interesting contrast between Ultron's high - tech abilities and their more basic, yet effective, methods.
One idea could be that April discovers a new hidden power within her extraordinary world. Maybe she can communicate with the long - forgotten creatures that live in the deepest parts of the world she inhabits.
A rival medicine cat from another Clan might be the main antagonist. They could see Alderheart as a threat to their own status or the well - being of their Clan. So they might use dark magic or some underhanded tactics to bring about his death.
Vilgax could be a great antagonist. He could hack into the gaming systems to try and defeat Ben in a virtual world where the rules are different. He might use his advanced technology to create digital versions of his minions to attack Ben.
The Organization in the Claymore world could be the main antagonist. They already have a lot of secrets and do some morally ambiguous things. If Naruto shows up and starts changing the status quo, like teaching Claymore warriors to be more independent, the Organization might see him as a threat and try to eliminate him.
It could be a new alien species that Ben has never encountered before. This species could be territorial and see Ben as a threat to their planet where he's stranded. They constantly try to drive him away or capture him, which makes it difficult for Ben to find a way to leave.
It could be a rogue ninja who was once a student of Orochimaru and has now developed his own dangerous jutsu. He wants to take over the ninja world and believes the old ways are holding everyone back.
Orochimaru could be a great antagonist. He might want to use Shenron's power for his own dark experiments. He could try to steal the dragon balls and manipulate the wishes to gain immortality or create an army of powerful, immortal ninja.