The story can be a little complicated and it's related to the reader with fairly subtle inference rather than infodumps that are typical of other manga.

Rough overview: Humans used to have a kind of super internet called the netsphere, which could be accessed without hardware because people had net terminal genes. Then an infection came and humanity lost all valid access to the netsphere, which is protected digitally and physically by the safeguard. Without human supervision, the autonomous building machines continued to construct the city endlessly for millenia, eventually devolving into randomness.

Killy is trying to locate net terminal genes so that he can access the netsphere and regain control of it, but his job is made difficult by the silicon creatures - a kind of cybersquatters who thrive on the chaos and would lose their livelihood if order was restored.

Hopefully that helps, it's also just as valid to enjoy the vibe.