"Which of you is going to use this pair of Mangekyou Sharingan to obtain the Eternal Mangekyō Sharingan?" Naruto asked the brothers, Itachi and Sasuke.
"Give them to Sasuke!"
"Give them to Itachi!"
Sasuke and Itachi spoke at the same time. Each wanted the other to obtain the Eternal Mangekyō Sharingan.
"You two really are brothers." Naruto chuckled, then turned to Itachi. "Your illness was caused by overusing your Mangekyou Sharingan. You should take them."
When Itachi looked ready to refuse, Naruto's expression turned stern. He exchanged for a Bloodline Fusion Scroll through the system. It could help Itachi obtain the Eternal Mangekyō Sharingan.
In the original story, Itachi had never obtained the Eternal Mangekyō Sharingan. Either he had wanted to leave his eyes to Sasuke, or a father's and son's eyes could not be fused—it had to be two brothers' eyes.
Naruto had asked Itachi about it before. The answer was the latter.
That was why Naruto wanted to help him through the system.
(Kishimoto never explained it in the original story, so consider it a rule of this book. Whatever the reason, and whether only brothers' eyes can be fused, it has little effect on this story's plot.)
As for why Naruto wanted Itachi to obtain the Eternal Mangekyō Sharingan, it was simply because Itachi was under the influence of Naruto's Kotoamatsukami. Of course he wanted his own side to be stronger.
Naruto beckoned to Sasuke, then turned and left.
Late that night, in Konoha.
The Sarutobi Clan and Shimura Clan compounds stood in the heart of Konoha, while the Uchiha Clan had been moved to a corner of the village after the Nine-Tails' attack.
Looking down at the two thriving compounds beneath them, Sasuke Uchiha snorted. "So this is Konoha?"
"Hah! That's Konoha for you!" Naruto laughed.