However, it could also be a new character that is influencing Iris to act in a way that Ash doesn't like. Maybe there's a mysterious trainer who has been filling Iris's head with wrong ideas about Pokemon training, and Ash has to stand up not only to Iris but also to this new character's influence.
Most likely, Iris could be seen as the main antagonist in this fanfic. Since the title says 'ash stands up to iris', it implies that Iris is the one causing some sort of problem that Ash needs to oppose. It could be her attitude or her actions that are creating conflict.
Another possibility is that there is no real 'antagonist' in the traditional sense. Maybe it's just a difference in opinions between Ash and Iris. But since Ash feels the need to stand up to her, it could be that Iris's strong - willed nature is being portrayed as something that Ash has to face, like an obstacle in their relationship.
Well, it could be that Ash has finally had enough of Iris's overbearing behavior. Maybe she's been bossing him around about Pokemon training methods. So, Ash decides to stand up and tell her that he has his own way of doing things and that he's been successful with it. For example, Ash might have his own unique bond with Pikachu that doesn't follow Iris's ideas.
It could be an evil sorcerer. This sorcerer might be after Noctis because of his special powers. He sees Noctis as a threat to his plan of ruling the world. The sorcerer could also target Iris because she has a pure heart, which he wants to corrupt, and Lemon because Lemon has a map that leads to a powerful magical artifact that the sorcerer desires.
Maybe the main antagonist is an evil scientist. The scientist has been studying Pokémon transformations and when he sees Ash turn into Pikachu, he wants to experiment on him. He chases Ash around, trying to capture him with all kinds of high - tech devices. This forces Ash to use his Pikachu form's abilities and his human knowledge to outwit the scientist.
There could be a mad scientist - type character who created the situation where Ash turned into a Latias in the first place. But then, this character wants to keep Ash in that form to study him and use his new - found Pokemon abilities for their own gain. They would be the main obstacle for Ash in his journey to turn back into a human.
Ash himself could be the main antagonist as he is the one doing the betraying.
A new, mysterious organization that is interested in controlling the legendary Pokémon. They see Latias as a key to their plan and Ash as an obstacle to be removed.
A powerful and greedy trainer who wants to capture Manaphy for its rare abilities could be the main antagonist. He might have a whole team of strong Pokemon and use underhanded tactics to try and get Manaphy.
It could be a rogue Pokémon trainer who wants to capture Ash - now as Pikachu - for his own collection. This trainer might have a cruel streak and not care about the well - being of Pokémon.
It could be a trainer who takes advantage of Ash's loneliness. This trainer might trick Ash into giving up his Pokémon or getting into dangerous situations. For example, he could tell Ash that there's a special place where he can find friends if he follows him, but it's actually a trap.
Team Rocket could be the main antagonists. They might hear about Ash's encounter with Mew and try to capture Mew for their own evil plans. They could set up all sorts of traps and schemes to try and separate Ash from Mew and steal Mew away.