A city's worth of people get stuck in a VRMMO world and their world has become a hodepodge mix of the real world and a game nobody seems to have heard of. Story is revolves around the community having adapted to this world and mainly focuses on a group of teenagers with attitude who have set out to defeat the supposed final boss of the game they believe is the cause of the mess.
When the group reaches what they believe is the final boss's lair, they instead discover a seemingly neverending cavern of computers that has logs events in their world. Looking through the records using the cavern's main terminal, they realize that they haven't been transported to another world but that their reality completely glitched out and that everyone in this new world are the remaining survivors from the event.
Completely freaked out by the truth, one of them desperately messes around with the terminal and triggers a humanoid interface mode that takes on the form of a robotic young girl. They quickly learn that the girl is essentially a god meant to readjust the course the world takes should anything ever go disasterously wrong. If they guide her along properly, they'll be able to bring their world back to its original state or even shape it to fit their ideals.
However, before she can actually make any drastic changes to their reality on a massive scale they must figure out how to lift the present restrictions on her abilities and ensure that she won't make things worse for them. Unsure of how to go about this, they bring her back to the city and thus begins their tale of fixing a broken goddess and their broken world.