The first big wrench in the plot is the arrival of an injured woman at the facility, after Daughter has been led to believe that no other humans except her still exist. This occurs after Daughter has already begun to question Mother thanks to the presence of a mouse in the facility — and you know you're starved for company when a mouse in the house excites you.
By the time the woman arrives, desperate and bleeding from a gunshot wound, tiny pinpricks have been poked in Daughter's understanding of the world — holes that the woman's presence, and the questions she raises, will tear wide open.
For the first time ever, Daughter's allegiances are tested. Who should she trust? The woman says robots like Mother are killers who destroyed the world, but after examining the woman's bullet wound, Mother claims the woman was shot by another human's weapon — not a so-called Dozer like herself.
When Daughter interrogates the woman, she's implored to seek out answers for herself, comparing the bullet inside the woman with one she shot at Mother. When Daughter does so, she learns the woman is telling the truth.
Digging deeper, she uses Mother's "fingerprint" to comb through other archives, discovering that Mother has also kept the existence of a previous daughter from her — one she killed and incinerated, just like the mouse, after failing her exam. It's one heck of a reality check. Daughter's allegiances shift dramatically, and things can never be the same.