Rath is a mysterious company affiliated with the Japanese government and Japan Self Defense Forces (JSDF). To achieve its goal, the company hired Kirigaya Kazuto to test a 4th generation FullDive machine, called the Soul Translator (STL). Unlike all other FullDive machines that came before, the STL connects to a user's Fluctlight (a quantum field that can be regarded as a human's soul), instead of the brain.
Normally things would progress to the point where Kirito would end up in the VR world Rath built themselves called the Underworld. Eventually, the people of Rath would take interest in one of the residents of the Underworld known as Alice and race to either protect or steal her away would ensue with all the parts involved having their reasons for trying to get Alice for themselves.
However that how things would normally go down as those at Rath only learn about Alice when it was almost too late to do anything about. Having planned to carry out something they had set into motion from the very beginning anyway. Though what if that was not the case as what if they did not discover Alice was there near their own end game. What if it was discovered earlier on that Alice was around and that they not only managed to acquire her far earlier where things were getting as dire be in the Underworld or in reality itself where they were facing several problems on their end as well from a raid on their main base.
In this scenario, they manage to advance their tech in using the Soul Translator (STL) to point where they have not only perfected sending in a person's Fluctlight into the Underworld, the VR world they created. They have managed to make so that they remove it from their body entirely and integrate into the Underworld. Thus making it an actual part of that world that would only exist there and nowhere else anymore. As for what they would do with that person's body that would be a story for another time at the moment.
The process to recreate someone Fluctlight ended mostly in failure cause the created one would most of the time have a break down after realizing they are not the original. Then someone came up with the idea of rather than making copies of someone else's Fluctlight why not just removed the persons and place in the Underworld not just to visit to exist there like all the others.
Despite what Rath had told Kirito their goal was the first bottom-up Artificial Intelligence, which could be used to pilot unmanned weapons. They considered that Alice was the first step in realizing that goal and in this scenario where they had gotten her earlier when nothing would happen for a long time now. The idea of just taking people's Fluctlights and making them in was being worked on. In this scenario, things had developed so that things went down that path.
Also since they had Alice now they were taking a far more hands on approach to managing the Underworld as there were massive changes that would happen to there for now on. The hands off approach that they were using were over as changes would be made on the fly and there would be constant meddling with the world and its people.
Although those of the Underworld would not care or more like they would not be able to care as taking a more hands on approach meant they could mess around with them at will as they were the creators of the Underworld thus it would make sense that they could do what they wanted with it. They could already speed up and slow down how fast time passed by. So it was possible that more direct control was possible to ensure things were going how they wanted.
Thus this is the story of all these things came to be and how different the Underworld starts to become once Kirito and friends are not just targeted to be taken into Underworld. No, this time although they would be trapped in this game there would be no escape or even desire to do so as they were placed in within the game to be players. They would be placed within the game to become a literal part of it themselves as being fully integrated into the system.