James has just learned that Michael has been working undercover for the CIA, but he also knows that Michael's allegiance now lies with his organization. Michael admits that while he may not always agree with James' methods, he does believe in his cause, which is why Michael's willing to go back to the CIA and lie to them on James' behalf.
Back at the CIA, the higher-ups are furious that the mission to apprehend James was a failure. They tell Michael that he has 48 hours to bring James Kendrick to justice, or Michael will be the one to pay the price.
Michael reports back to James that the only way the CIA will be satisfied is if Michael can bring him into custody. James, recognizing he's been exposed, tells Michael to go ahead and hand him over to the CIA. Michael and Sonya will take over his organization once he's gone.
Wanting to keep his friends out of this, Michael asks Sam, Jesse, and Fi to stop helping with his mission. Fiona, surprised by Michael's sudden change of heart, becomes suspicious and plants a tracker on him. Sam and Jesse use the tracker to follow Michael to a secret meeting with James, where they learn that Michael has indeed switched sides.
To save Michael's soul and keep him from being swept up by the CIA, Michael's friends decide to kidnap him and take him far away from Miami until everything blows over. Kidnapping Michael Westen turns out to be no easy task and Michael escapes back to James and Sonya.
In the end, the only chance the team has to stop Michael from betraying everything he's ever cared about is for Fiona to put herself directly between Michael and his new life.