The Authority planned on continuing the original plan from NOiSE.While their original plan was halted due to the efforts of The Order throwing the Net-Sphere into Chaos by infecting humans with Net-Terminal Genes with some sort of gene-altering virus, they never forgot their long term plan. As The City continued to expand and The Safeguard began exterminating humans indiscriminately for not having Net-Terminal Genes, The Authority had to take action to preserve what was left of humanity, secure the Net-Terminal Genes, and halt The City's expansion, all so they could set the original plan back in motion. To this end, they awoke Killy and two other beings similar to him (as seen in his flashback while regenerating) and sent him on his mission. 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.
Killy was (or was manufactured based off of) the protagonist of a Harem Genre series at some point in the past.It'd explain how he's so durable with so little apparent cybernetic modification.