I'm going to be honest with you. Aside from that show being about MMO's.. I have no idea what any of it contains.
Basically, the developer of the game left a piece of himself inside the game, as the form of his daughter he could never have, and the game code itself is trying to erase it from existence as it has become sentient AI (and think it is a virus).
The players get caught up in this as they are "flagged" as viruses as well, and somehow traps their minds in the game world (don't ask).