Thing is that I realy wanted to talk about him...
What is he exactly? As I have seen Killy and his GBM (gravitonal beam emitter) are evolving trought time... Ok, like this it sounds stupid but...
In the start Killy was showed as human with cyber implants. He was reading a book, he was eating and sometimes got realy busted. Same with GBM - yes it is powerfull from the beggining but later on it changes.
Killy doesn`t need to eat, he can jump from few hundred meters, punch trough the walls and so... later on (before Dhomochevsky part) there is time passed from startig the mission - 267years have passed! And even later when LEVEL 9 SG Cibo made that explosion 40.84% of his body was destroyed and then he is showed as complete cyborg...
Same stuff with GBM - later on even Level 1 beam is much much stronger and is making bigger damage then in the beggining...
So - can anyone tell me someting how you are looking at that stuff...

at the beginning Nihei don't have very defined history and for that reason maked that Killy could eat or the firings of their pistol were different

In the artbook say Nihei that Killy its the most powerful cyborg in his world, he is a secret agent from a different and superior system than Safeguards.

Well that is only possible ansewr... Damn, I only don`t have artbook - I want in english becouse I don`t know German or Franch that well so I can understand such text...
It`s all there about the world of Blame!, right?

i think that in somewhere is a translation of the artbook to english, but its incomplete...
Although its a great work, well i find now:
http://www.angelfire.com/comics/jenshin/blame.html

OK, that's cool. I'm just trying to see if I got the plot wrong. On what page does Dhomo say they invaded "a few years ago"?

What follows is my opinion:

Killy didn't realise he was a cyborg to begin with. He implied that when he was travelling with the cargo ship, saying "My growth period has long since finished." or something to that effect. This meant that he didn't know he wasn't human, or just special since he stopped growing older. His cyborg brain (might not be completely organic, as it's not a prerequisite for cyborgs to have completely human brains) would have kept important information, or mission objectives:

Search for a person with NTG.
How the GBE works.
SC are evil creatures and cannot be trusted.
Take drugs whenever you are injured - This is referring to his administering drugs whenever he was injured in the early logs. This might've been nanobots to inject into his system to repair himself without his control, as his cyborg abilities were not awakened. However, he probably didn't know this, and just thought it was natural for him to take them.

He didn't know of the GA as yet, and when he first met them he assumed it was the enemy. The time when his SG abilities emerged was after Sanakan injected him with the needles. She was invoking the SG to emerge within him. Still feeling weak, he eventually woke up from his healing, and had his optical sensors enabled. He could then scan for the net terminal gene automatically, and Sanakan knew this, as she stated that his "functions were restored". Note that from that time he never injected drugs again. He was more able as he knew what he was, and had begun to use his body to its full effect, healing himself when necessary, taking hits knowing he could heal, and his new photographic memory.

He even rejected the registry with the SG, as maybe he realised that they weren't what he wanted to become, and that 3000 years of living as a human finally made him choose to live as a human, and not as a SG killing other humans.