A rogue ninja who wants to steal the power of the contract for his own evil purposes could be the main antagonist. He might be jealous of the connection between Sakura and Itachi and wants to break it to gain the abilities they could potentially unlock together.
Itachi himself could be seen as the main antagonist in this scenario. After all, he is the one doing the kidnapping.
Itachi himself could be seen as the main antagonist in this scenario as he is the one carrying out the kidnapping. He is acting against Sakura's will and causing a dangerous situation for her.
It could be Orochimaru. He's always had an interest in powerful shinobi, and Sakura has shown great potential. Itachi might be roping Sakura's wrists to prevent Orochimaru from getting to her and using her for his evil experiments.
A rogue ninja from a rival village could be the main antagonist. He might be after the secrets of the Sharingan that Itachi and Shisui possess. And he sees Sakura as an obstacle when she tries to protect her comrades. He could have some powerful and forbidden jutsu that makes him a formidable foe for the trio.
Maybe it's an ancient evil that was sealed away long ago and the colossus contract is the key to its release. This evil force would be the main antagonist as it tries to break free and cause chaos in the ninja world. It could be something like a powerful demon that was once defeated by the first Hokage but is now on the verge of coming back because of the colossus contract. Naruto would have to stop it with the power of the colossus.
In this fanfiction, the main antagonist could be a strict teacher. Sakura, being a boy with a free - spirited nature, often clashes with the teacher's rigid rules. The teacher always seems to be out to get Sakura, giving him unfair punishments and trying to suppress his creativity or individuality.
Itachi himself could be seen as the main antagonist in this scenario as he is the one performing the kidnapping. His actions are against Sakura's will and are likely to cause distress and conflict.
The Akatsuki could also serve as antagonists. Even if Itachi was once part of them, they might target Sakura to get to Itachi or to use her skills for their own evil purposes. Their goals of collecting tailed beasts and causing chaos in the ninja world would clash with Itachi and Sakura's efforts to protect the village and each other.
Another possibility is that an old enemy of the Uzumaki clan resurfaces. They use Itachi's complex relationship with the village and his own motives to manipulate him into kidnapping fem Naruto. So, this old enemy would be the main antagonist as they are the ones driving the overall conflict.
It could be Danzo. In the original story, Danzo was a major factor in the Uchiha massacre. If Itachi goes back in time, Danzo would likely still be plotting against the Uchiha. His thirst for power and his extreme methods would put him at odds with Itachi's new attempts to save the clan.