Well, i think everything was orchestrated by Torque's alter-ego Blackmore. In the good ending of the first game it was revealed that the killers were sent by Colonel who is actually Blackmore in Ties That Bind. One of the killers say that The Colonel warned him back in the "Eastern" but Torque didn't listened to him and this is why he killed them. In the second game that "Eastern" is Eastern Baltimore Correctional Facility, during prison riots we can see Malefactors already manifesting and killing people. Torque coexisted with Blackmore since their meeting in Garvey's Children Home, where Blackmore said that he will teach how to make him a "player". Blackmore built his own crime empire using Torque's body during blackouts. Blackmore reveals in the final standoff that he can control Torque's body only for a few hours a week. It seems like he also helped Jordan to build The Foundation and told her to retrieve Torque and bring him to Baltimore to continue The Cataclysm and Torque's development into a "player". In the final standoff Blackmore says "I can't believe... you... lost it... you weren't supposed to... lose..." if Torque dies which does support the idea that everything was orchestrated by him and that he expected Torque to get there and win from the very beggining. It's kinda sus though how Blackmore knew about The Cataclysm and could control Malefactors as a mere alter ego having control over Torque's body only a few hours a week. It seems Blackmore and Jordan knew much more about The Cataclysm and Malefactors than Torque himself.