The scenes where the Major meets with her mother. Special mention goes to the ending, where the Major visits the grave of her past self Motoko Kusanagi, and afterwards hugs her mother, telling her she no longer needs to mourn her now-found daughter.
The Major's mother removing all of the protective plastic covers from her daughter's room.
The Major and Batou get a lot of fun snarky lines back and forth, but each of them repeat a particular line during vulnerable moments after being injured:
Say something nice?
The Major climbs out of the water after going for a dive and finds Batou hanging out in her boat. In a moment of paranoia, she asks if he'd kill her if ordered to. His reaction of indignant anger at her even considering the possibility is enough to reassure her. Even if she knows nothing else for certain, The Major knows she can trust Batou to have her back.
