Their exploration and getting further from the mission triggered the system and the person who was in control of it.
Seeing Lucas act on his own and lead his teammates, not to the way the system wanted to, made the system do something that it hasn't done since Izek's revolution began.
It took a lot of time for it to find a new player to accomplish the missions, many things had changed and made the plot different and that's why it was there to help Lucas win.
But now, more characters showed up, and the more things went left and wrong, the more it became suspicious of Izek's return.
The system thought that sealing Izek inside his own made energy pills, will make him disappear forever, but it failed. The more pills were being used, the harder chances grew that he will come back.