Cibo either knew some fragments of The Authority's original plan or was working against them on general principle (she seemed to have a contempt for authority and boisterous, Chaotic Good attitude when first introduced). This would explain why she transcribed the Net-Terminal Genes onto herself during the Level 9 incident. This would also explain why Sana-kan insisted she not trust The Authority when she found Cibo Post-Level 9 and The Authority's antagonistic role towards the end as they allied with The Safeguard to take The Sphere which held the Net-Gene Child. Killy is largely unaware of what is going on but apparently is protecting the Net-Gene Child until she grows into adulthood and can halt the growth of The City on her own terms instead of being apprehended and "re-educated" by The Authority and The Safeguard to suit their purposes (such a thing might be in their programming for orphans or persons of interest).
Net-Sphere Engineer and Blame! 2 imply that humanity is now back on its feet and is now disconnected entirely from The Net-Sphere, free to continue its existence without oppression, no doubt due to the Net-Gene Child's actions.