A new teacher who is secretly a dark wizard could be the antagonist. They might have come to the school with the intention of stealing Twilight's powers. By locking her in the school, they can have more time to try and carry out their evil plan without interference from the outside world.
It could be Danzo. He was always power - hungry and had his own ideas about how the village should be run. He might see Naruto as a threat to his plans, so he locks Naruto away as a baby. He wants to control the village without the interference of the jinchuriki's power.
It could be a vengeful Death Eater. Maybe Draco once crossed this Death Eater in some way, and now the Death Eater wants to teach him a lesson by locking him in a cage. This Death Eater might be jealous of Draco's status in the Malfoy family or his closeness to Voldemort at one time.
It could be a new vampire who is jealous of Edward's relationship with Bella. This vampire might be from a far - off place and has heard about the Cullens and Bella. They decide to kidnap Bella to make Edward suffer. Another possible antagonist could be a human who has a grudge against the Cullens. Since Bella is associated with them, they target her. For example, a human whose family was attacked by a vampire in the past and blames the Cullens for not preventing it. They think that by kidnapping Bella, they can get back at the Cullens.
It could be a powerful vampire from a different coven. Maybe one who sees the daughter of war as a threat to their power or territory in the Twilight world.
A secret organization could be the antagonist. They might see Bella as a threat to their hidden agenda. For instance, if she has stumbled upon some information about their illegal activities, they lock her in a room to keep her silent and prevent her from sharing what she knows with the outside world.
One possible plot could be that Twilight discovers a hidden magical realm within the school. Maybe there are ancient spells hidden in the school library that she stumbles upon while locked in. Another plot could involve her having to solve a mystery that's tied to the school's history to find a way out. For example, there might be a ghost haunting the school and she has to figure out its story to break the 'locked in' curse.
It could be a dark magic user who doesn't want the human - turned - Twilight to succeed. Maybe this antagonist sees the new Twilight as a threat to their own power or plans in the pony world.
It could be the Queen of Hearts from Alice in Wonderland who has somehow gained new and dark powers. Maybe she wants to conquer not only Wonderland but also Naruto's world. She could use her army of playing cards and newfound magic to create chaos.
It could be Ares. He might see the Twilight vampires as a new source of power or chaos. He manipulates Percy into believing that the Twilight characters are evil and need to be stopped. So Ares becomes the main antagonist as he's the one driving Percy to betray the Twilight group.
The Volturi could be the main antagonists. In the Twilight universe, they are the powerful vampire coven that enforces the vampire laws. They might see femNaruto's presence as a disruption to their carefully maintained order. Her different powers and her way of thinking could be a threat to their authority.