Thornton is tasked with making sure Bozer is not a threat to national security. The rest of the Phoenix Foundation crew (Mac, Jack and Riley) head off to Latvia to capture a terrorist.
The terrorist foils their plan and engages them in a shootout outside a bank. They take him into custody, but not before he lets all of his terrorist friends where to find him. Soon they are running toward the United States embassy for protection.
Once they are inside, they must figure out a way to hold off the rebel group until reinforcements can get there in six hours.
MacGyver uses a physics equation to stop bullets from entering the building, but soon it becomes clear that they will be unable to hold off the attack much longer. So Mac “invites” them in so that they may trap the bad guys inside the embassy lobby while the staff sneaks out by way of a rope ladder from the the second floor.
Back in LA, Thornton is ready to let Bozer finally go home, but there’s a hitch. He has to agree to work in the lab of the Phoenix Foundation. Bozer also forgives Mac for hiding his true identity.