Air date: 3/23/09

Chuck reluctantly tells his handlers that he has been contacted by Orion, the mastermind behind the Intersect computer and the person who can erase the Intersect from his brain. When the team goes to retrieve the computer Orion sent to Chuck, they run into a Fulcrum agent named Vincent. After Orion's computer is brought back successfully, General Beckman arrives in person to oversee the operation to locate Orion. At Orion's urging, Chuck goes to meet him but is forced to betray him to Fulcrum by Vincent. After seeing a Predator drone destroy a Fulcrum helicopter, Chuck is upset that Orion had apparently killed himself. Back at home, Chuck receives the schematics of the Intersect from Orion. Meanwhile, a conflict breaks out between the Burbank and Beverly Hills Buy More branches.

Chuck vs. the Broken Heart

Air date: 3/30/09

Worried that Sarah has become too close to Chuck, General Beckman sends Agent Alex Forrest to assess Sarah's performance and to act as Chuck's temporary handler. The team steals Devon's hospital key card in order to plant a bug in the pacemaker of an Afghan terrorist. However, their plan backfires when the terrorist's personal physician discovers the bug and kidnaps Chuck, thinking he is the surgeon responsible. Sarah, after being dismissed by Beckman, finds Chuck and helps Casey and Forrest to rescue Chuck. Noting that their close relationship may be an asset, Beckman reinstates Sarah as Chuck's handler. Having located Chuck's long-absent father, Sarah takes Chuck to meet him.

Chuck vs. the Dream Job

Air date: 4/6/09

After some initial resistance, Chuck's father Steve Bartowski returns home with Chuck to see Ellie. Upon discovering that Fulcrum is planning to release a computer virus at the launch of the new Roark Instruments (RI) operating system, Chuck infiltrates the company by landing a job that he has always wanted. However, he loses the job after he tries to stop RI's founder Ted Roark from proceeding with the launch. Despite Chuck telling them that Roark has an Intersect, Sarah and Casey refuse to help him find it without proof. Chuck goes alone and on the way, he is aided by his father, who turns out to be Orion. They try to use Roark's Intersect to erase the original Intersect from Chuck, but fail. Steve is captured by Fulcrum, who wants him to finish building Roark's Intersect.

Chuck vs. the First Kill

Air date: 4/13/09

As a last resort, Chuck enlists the help of his ex-girlfriend, the imprisoned Fulcrum agent Jill Roberts, to find his father. Jill and Chuck pose as an engaged couple at her parents' home to meet her Fulcrum recruiter Uncle Bernie. Instead of helping them, Bernie tries to kill them but dies from a heart attack before he is able do so, leading Casey to call it Chuck's first official kill. The team tracks a call to Bernie's phone to the office building where Chuck's father is being held. Although the team fails to retrieve Chuck's father, Chuck lets Jill escape after she fulfilled her end of their bargain. Sarah disobeys General Beckman's orders to bring Chuck in to be locked away and instead goes on the run with him. Meanwhile, at the Buy More, Emmett betrays Morgan and uses him to get promoted to the manager position, causing Big Mike to get demoted.