Shinji hadn't realized it at first. Only after noticing the urgency Utatane Koharu was hiding did he belatedly start to suspect something.
In the original timeline, after Pain attacked Konoha, Danzo seized the Hokage Position while Tsunade was gravely injured. It could be considered the Advisor Elder Council's final counterattack.
After Danzo died at Sasuke's hands, the two remaining Advisor Elders, Utatane Koharu and Mitokado Homura, were quickly sidelined.
But the Third's influence was far greater now than it had been in the original timeline.
Jiraiya and Tsunade's strong return, along with the rise of newcomers like Naruto and Yakumo, had accelerated the Advisor Elder Council's loss of power.
Once Shinji understood this, all his earlier doubts were resolved.
"Should I agree to her offer?"
Shinji hesitated.
He and Utatane Koharu could be said to be joining forces for their own purposes. He needed her, a village Advisor Elder, to help him handle trouble, while Utatane Koharu needed him, the Ninja Academy's top student, to secure her position and extend her influence.
But their needs were not equal.
Utatane Koharu's power wasn't indispensable to Shinji. After more than a year of growth, he had long since left behind the precarious state he'd been in when he first crossed over. The threat the Konoha High Command posed to him had been greatly reduced after he fused with the Eternal Mangekyo Sharingan.
By contrast, he was indispensable to Utatane Koharu.
At the Ninja Academy, Shinji was the only one who could suppress newcomers like Naruto and Yakumo, protégés of the Third, and who could also be controlled and won over. She had no other choice.
So, just as Utatane Koharu was sitting back, confident she had Shinji in the palm of her hand, he calmly bowed and said, "I refuse!"
Utatane Koharu's