Perhaps it's a powerful criminal organization. They know that once Sam Fisher is fully trained by Bud, he will be a major obstacle in their illegal operations. So, they send their best assassins or hackers to try and stop the training process, or even capture Sam Fisher to use him against his own side.
It could be a rival agency or a rogue agent from within their own organization. This antagonist might be trying to disrupt Sam Fisher's training because they see him as a threat to their own power or plans.
Perhaps in this fanfic, Bud is training Sam Fisher for a very dangerous and secret mission. They start with basic training like endurance building, weapon handling, and then move on to more advanced skills such as silent infiltration. Bud could be passing on his years of experience to Sam, and Sam, being a quick learner, is constantly evolving in his skills under Bud's tutelage.
It could be Orochimaru from the Naruto universe. He might be interested in the cat's special abilities, perhaps thinking he can use them to gain more power or immortality. He would be a formidable antagonist as he has his snake - like powers and is very cunning.
Vlad could be a great antagonist. He might see the baby versions of Danny and Sam as an opportunity to finally get rid of Danny for good. He could try to use their weakened state to his advantage and steal Danny's powers once and for all.
It could be a rogue ninja who has a special ability to disrupt shadow clones. This antagonist might be jealous of Naruto's ability to use shadow clones for training and wants to stop him. Maybe he has a jutsu that can make Naruto's clones go berserk and attack him instead of following his commands.
Well, it could be that there is no traditional antagonist. Sam's betrayal could be the main source of conflict, and she could be seen as the antagonist in Danny's eyes for that time being. But if there has to be another force, it could be the entity that influenced Sam to betray Danny in the first place. For example, a powerful and manipulative ghost that has its own agenda and uses Sam as a pawn.
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.
A powerful demon who wants to take over Crowley's territory might target his daughter. By getting rid of her, they believe they can weaken Crowley and then take what he has. This demon could be very cunning and use all sorts of tricks to get to her.
It could be a rogue ninja who has been secretly observing Naruto during his training trip. This ninja, jealous of Naruto's growth, decides to target him and the village he protects. He has some unique and dangerous abilities that even Naruto's new - found power will have a hard time dealing with at first.
The main antagonist could be an unknown enemy that has a vendetta against Jiraiya. They might target Naruto during the training as a way to get back at Jiraiya. This enemy could be someone from Jiraiya's past, perhaps a former student who turned evil and blames Jiraiya for their misfortune. So, they see Naruto as a way to hurt Jiraiya deeply by killing his pupil during training.
A young peasant boy with great potential could be a main character. He is chosen from his village to go to the castle for training as a knight. There could also be an old, grizzled knight as his mentor, guiding him through the tough training regime.