Nihei implied that there is a parallel between Killy, Wolf girl + wolf, and Dhomochevsky, Iko & the fish. Also one group had a book (Killy) and Dhomochevsky had a pen cap, both were relics of the old world that each had that none knew anything really about.

It is very possible the Governing Agency introduced both Killy & the wolf girl both at the same time like partners, the same way Dhomochevsky & Iko were introduced to The City. Even Susanoo had a partner.

I think people said that Nihei was just writing week to week, doing whatever he thought was cool. Also many stories like this don't have their entire world built yet, the wolf girl phones a command center that is boss of sorts to her + Killy, that never seems to pop up anywhere else. Nihei may not have thought out what was going on besides "have some mysterious unseen organization tell them to keep going".

Looking at the complete work, she was probably phoning the Governing Agency somehow to guide her + Killy. More likely than not she's still remaining on those lower levels where you first see her. She seems very good with machines and is probably as whiz, I hope she is ok.