[Spoiler] 2B Question - Ending C/D

The game is clear on how 2B, truthfully 2E, is designed to kill 9S when he uncovers the secret behind humanity and YorHa. Maybe I missed it, but how does she know when she is supposed to? I forget exactly but I thought all androids on the bunker (excluding the commander?) do not know about humanity's secret. Does this imply that 2E knows the truth already? I don't see how she's supposed to know when to kill 9S if she does not know humanity is gone already. Did 9S avoid execution by discovering the secret while they were separated? I don't remember the two of them ever having a conversation about it, only 9S contemplating telling her.