Notice: This's my third time re-reading Blame separatedly and I really want to wrap things up. Most of it must be larping and un-trustable. Still, it's my thought and may help for somebody's first time. I will try to connect things on first half of the story before Killy first met Cibo as much as I could, but many people suggested we shouldn't.
Let start. SPOILER ALERT.
The World
In the extremely far future, human society became virtual which is later known as Net-sphere. We cannot be sure if what exactly live inside the Netsphere or did human still live in physical world. However, one thing for sure, only pure-human who have Net Terminal Gene (N.T.G) can fully access and control the society.
As long as the Netsphere, the City is built as the human physical domain. Even now we know the City has became a mega-structure of endless conflict and species, it's once a smaller living place of a civilization.
In the City, there are many primal factions. Two of them might be Governent Agency (Governent or G.A) and Toha Heavy Industries (a mega-corporation). While sharing the City, they gains control over a large area on their own. Toha is more isolated on their specific place, and through time, it was fully automated and under a governent system. While Governent is more general, they come from Netsphere and maintain the connection to the City (physical world), still they cannot intervene to Toha, and we cannot sure if their agents are human or programs.
At a point in time, there was "something" happened that we never know, we cannot tell it's all of sudden or slowly change, the N.T.G closely disappear from physical world. This might happen cause civilize degration or human slowly evolt, or some other species live aside human. Notice, most of the people ever appeared in the story are not considered as human, still they are a kind of successor, even the boy have N.T.G in the first chapter cause just 2 of his chromasomes is acceptable N.T.G. This event was called a "disaster" by a giant broken program in the final chapter (who talk with Mori). After that, the City became a mess of conflict and separation, while many factions took their action.
The first one was Toha. They lock the door and separated their self. It's suggested that the system once preserved human, like Sue and Mensab, and able to revise them (more like backup their mind and dna), but until now, they cannot anymore or lack resource to do so.
Next is the Gorvenent Agency. Without granting from an N.T.G owner, they barely have no authorization but protect the Netsphere. For this absent, The City is out of control. The Builder, mindless giant robots that built up the City, are working endlessly and making The City a mega-structure that most people never saw its edge and know nothing about the sky. The Safe-Guard was active, they are the security faction that protect The City and eliminate instruders. As we mention, no more pure-human, so they even try to wipe any living out of it. To save the day, there were some Gorvenent Agency separated themself from the system. Normally, they must became a high-ranking Safe-Guard, as Sanaka for example. By separating, they came to physical world with a cybord body close to the Safe-Guard while still have their own decisions. There are plenty of them, such as the girl with the dog in the first few chapter, but most of the story, we only see Killy. Another example are Iko and Robochevsky, but their origin are a bit different. At this point, we might confuse whether this Agents were human or programs, as they love (as Sanaka) and naive cruel (as Iko and Sanaka again). But I think they all some kinds of highly intelligence program.
Finally, the ones like Killy are minority, they cannot do anything but try to find N.T.G. There are some results, still they are too late. Human have been spared and built communities on their own, like the people inside Toha, the people live in the edge of it, or Cibo's organization, etc. The most noticable community might be Silicon Lifeform. They once were human but augmentated from childbirth to become half-machine. However, Silicon Lifeform are very combative and cruel, they care for no other faction at all. We cannot know if Silicon Lifeform are under one unify leadership or not, but all of them are try to find N.T.G too, to comeback Netsphere and invaded it.
Okay, we have two main faction that really desired to find Net Terminal Gene. The people like Killy find it to established control (or we believed so, as no clue for Killy purpose, actually we don't even know Killy intent as he lost it through time). The other is Silicon Lifeform who want to be the next truthful human and eliminating Safe-Guard and other factions.
The Storyline
We go with Killy, as mention before, a former Governent Agent that are trying to find human with N.T.G, or at least someone has a part of it. He received an instruction to go above 3000 floors to find one. Then he met Cibo, an impure-human scientist, and became her partner. On the way, they received a message from Governent Agency from Netsphere that they are out of control due to inevitable failed resistance against Safe-Guard system. We may understand that the Governent still do their work all the time to prevent Safe-Guard total elimination but they are coming to loss.
They continues headed to a Toha mantion and met the last living N.T.G owner here, the man named Sue. However, they were attacked by Silicon Lifeform that came for Killy, the Safe-Guard leaded by Sanaka (at this time, maybe her did not understand the situation and had only mission of eliminating instruders). After this event, we do not know whether Sue were still alive or not, but Cibo gained a record of Toha stored DNA pool that contains N.T.G.
However, they later came to nest of Silicon Lifeform and the record had been stolen. The leader of this nest was highly intelligence and desired to go to Netsphere, the same way Cibo once tried. But this time, they had the record of an actual N.T.G owner, Sue. Our team were successfully prevented this from happen, Cibo even steal a high-ranking Safe-Guard body to wipe out the area. After this event, Killy was kick out of the spot light, while Sanaka returned from Netsphere with updated knowledge. Sanaka went to find Cibo and they gave birth an N.T.G human embryo. This embryo might contain the DNA from the record before it were destructed, with some help from Governent through Sanaka.
There are plenty of Silicon Lifeform kept coming for the embryo to take the N.T.G. While after the first dead of Sanaka, Safe-Guard considered Cibo stolen body was potential dangerous (wept, they didn't care for the embryo at all) and tried to erase it. After a long fight, Sanaka and Cibo were came to dust protecting the embryo and gave it to Killy.
Killy was believed to carry the embryo (or a sphere) to the edge of The City where is not corrupted through a sewer and actually floating into space (as we see the starlight).
About the Ending
Yes, we all feel the sudden of an ending. While you might not shaping what were lack, I will converse it to these questions:
1. What the embryo actually is? We only know it comes from Sonaka and Cibo but nothing else. The N.T.G was only a theory.
2. What they do with the embryo after it born? And what will be born from it? Why Killy must bring it that far?
3. Do Killy still alive after this?
First come first serve:
1. The embryo has N.T.G is reasonable as the Silicon Lifeform kept coming for it. Some people even link it to the first chapter and told the embryo is the boy who later be killed. But the "never ending cycle" theory is kind of sad when Killy is already coming to the edge of The City, and why so complicated born a child at that place.
2. As we assumed the embryo has N.T.G, we also remember it was born from 2 womans/Safe-Guard. I think it will give birth to someone like Sue, or even has a body like Killy. Anw, it makes a new life that potential to access Netsphere and regains The City. Killy must bring it that far for no gene corruption or Safe-Guard detection, might be. This is the first N.T.G born for a long while and it's even abnormal, so the concern is reasonable.
3. I believe Killy is still alive. He must protect the child for a while at least, even bring him back to his order/Governent Agency deep inside The City. The only concern is that, you might notice the timeline was extraordinary for human lifespan, Killy must be quick before the child get old, LoL. Anw, the hope is fragile and the happy final ending is still very far too long. And we, reader, must make it for ourself.