General Beckman sent four agents to Castle for Chuck to choose from to become the new Intersect. After strenuous testing Chuck, who has now been labled as the leader of the team, chooses Brody. Brody is then killed. The Team must figure out who killed Brody. After another agent is wounded and another killed, there are only two left. Chuck decides that it is not the female agent or Director Bentley, and figured out it was the original wounded agent. He solves the mystery and saves the Team from the bomb that the murderer brought into castle.
Meanwhile the Buy More crew is in a prank war with Large Mart. Jeff and Lester stole Large Mart's pig, Kevin Bacon. In retaliation, Large Mart stole Big Mike. Even though he is doing fine, eating Subway sandwiches, Big Mike needs to be rescued by Morgan and company. Morgan wants to give Kevin Bacon back, but Jeff and Lester release him into the air ducts. Big Mike ends up escaping on his own and making his way back to Buy More.
Ellie continues to use the Orion computer, learning more and more stuff about Stephen's work with the human brain. Awesome tells Chuck, who then decides to get Awesome to switch the computer's hard drive with a blank one. Awesome pretends to switch it and makes chuck think that he went along with the plan. Ellie and Awesome continue using the computer, and while she's sleeping, the computer scans her brain.