NieR Automata Ver1.1a - Episode 3 - Shirei-Kan

The YorHa Commander watched 2B and 9S's progress from her orbiting space station. She was impatient.

The end credits for NieR Automata show how much 2B cares for 9S. I don't get why, either.

2B and 9S joined humans on their current mission. The humans thought they were sent by the humans still on the moon. The YorHa Commander allowed her androids to play into the resistance fighters' confusion. The android team needed to investigate odd robot behavior and found enemy bots had made humanoid bodies!