Naruto could be one of his allies. Naruto has this knack for seeing the good in people and would probably be willing to give Obito a chance to redeem himself. Also, Sakura, with her skills as a medic - ninja, could be an ally. She might help heal Obito if he was injured during the war and see the potential in him to be a force for good.
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The fanfiction could explore how Obito's identity revelation affects his relationship with the Akatsuki. Some members may feel used or deceived, while others might see it as an opportunity. It could also show how Obito's true self starts to form new bonds or break old ones within the organization, depending on how his true intentions are perceived.
One possible motive could be to use Sakura as a bargaining chip. If he has some sort of plan against Naruto or the Hidden Leaf Village, Sakura, being a close comrade of Naruto, could be very useful. He might think that by restraining her, he can force Naruto to come to a certain location or make concessions.