James eventually tells Michael, "The CIA has to question threats; I eliminate them." Working with Sonya, Michael carries out a number of missions, including the one that Burke was working in the Dominican Republic before he sacrificed himself. Though many of the methods used in the missions torment Michael, he carries each out, often at Agent Strong's prodding. Eventually, Michael and the CIA have their opportunity to capture or kill James and Sonya, but when Michael finds Simon Escher heading up a capture team and that Simon has been working off-the-books missions for Strong over the past two years, his idyllic vision of the CIA comes crumbling down. Michael helps James and Sonya escape, and after James blames Sonya for leaking their location and points a gun at her head, Michael finally blows his cover. Despite his infuriation, James realizes Michael could have completed his mission and freed his friends but didn't, and he spares him after Michael convinces him that he no longer believes in what the CIA is doing. James then realizes that, with what the CIA now knows, he will continue to be hunted. He arranges his own "capture" at the hands of Michael, with the understanding that Michael and Sonya will head up his organization while Michael continues the façade of working for the CIA. Michael agrees, and even believes that such an arrangement would work; he could do good things without the restraints of CIA rules and leadership. But when Michael sees that Sonya is willing to kill Fiona for being a "threat", he finally realizes that the organization doesn't just operate without rules, it operates without a conscience. Though Michael is on the run from both James and the CIA, he chooses to take out James' organization. Michael, Fiona and Sam raid James' satellite uplink facility to collect a hard drive containing information on James' organization but he sends his forces to Maddie's house and threatens Michael he will harm her if any threat comes to his operation. Maddie sacrifices herself to protect Michael, his friends and Charlie. Ultimately Michael tracks down James and fatally shoots him, but before dying he pushes a dead man's switch that blows up the whole building. Sam escapes with the hard drive while Mike and Fiona fake their deaths. Sam and Jesse later deliver the hard drive to Strong which leads to the capture of over 100 members