Because [spoiler=MLA]he doesnt just remembers Alternative's Meiya , he remembers all 3 Meiyas he met (extra , unlimited , alternative) and all those memories were still there , he didnt want to accept the fact that he had to do it for the mission because he wanted to save that meiya if possible , even knowing that killing her was the right thing to do for the mission and to give her a mercy kill since she was contaminated by the primary target. he didnt want to lose anyone in his squad , and killing her made him feel responsible for everyone's death , considering he saw Miki's corpse just a fe