when kakkashi killed Rin mangakyo awakened in him but didn't noticed about that and the awakened mangakyo would have been faded since he didn't give much thought about that. Naruto came after three years to konoha and Tsunade said that she didn't give any mission to kakkashi after they have gone.The reason why kakkashi didn't get any mission from Tsunade is because he awakened mangakyo.This time kakkashi wanted mangakyo is because its a good weapon against Itachi and rest of the members.He thought like that.But he noted that he is slowly moving towards blindness.
This is the time he need a help from Tsunade.She is a medical specialist and would have done some thing to kakkashi's body. So that Kakkashi's fast going to blind ness would have become slow. Thanks to Tsunade.So in order to work her treatment kakkashi would have took a three year leave from missions