The team tracks a call to Bernie's phone to the office building where Chuck's father is being held. Having located Chuck's long-absent father, Sarah takes Chuck to meet him. Meanwhile, Anna wants to move into an apartment with Morgan forcing him to finally act like an adult. Although the team fails to retrieve Chuck's father, Chuck lets Jill escape after she fulfilled her end of their bargain. Meanwhile, corporate efficiency expert Emmett is out to get Chuck and interrogates Morgan to get some dirt on his best friend.
Morgan's reluctance to live with his mother while she is in a relationship with Big Mike leads to Chuck and Morgan deciding to move in together. While Sarah and Casey are engaged in a gunfight, Chuck goes into the Intersect room, where he finds Bryce with a fatal gunshot wound. In an attempt to save face, he lies to the girl who broke his heart and tells her that he is more successful than he really is. In the wake of his disbelief, Chuck is asked to use his relationship with Jill to get to an agent called Leader. Sarah disobeys General Beckman's orders to bring Chuck in to be locked away and instead goes on the run with him.
Meanwhile, Morgan offers Devon some advice for a romantic night with Ellie, and Lester struggles to gain respect at Buy More as the new assistant manager. After locating the lab of Perseus, Chuck learns that a man code-named Orion is the designer of the Intersect and headed the entire Intersect project. Chuck does his best to reassure Jill that his relationship with Sarah is purely business but only finds himself in more trouble when Jill finds Chuck and Sarah in their hotel room in their underwear after trying to wash off a suspected bioweapon. Meanwhile, at the Buy More, Emmett betrays Morgan and uses him to get promoted to the manager position, causing Big Mike to get demoted. The team retrieves Steve and the new Intersect before the Fulcrum base is demolished by an airstrike.
Chuck is told that this successful mission marks the end of his espionage career and the beginning of a normal life. Archived from on March 14, 2012. Chuck and Jill embark on another romantic getaway, during which Sarah and Casey discover from the recovered list that Jill is Fulcrum herself. Beckman declares their operation to be over and Morgan quits the Buy More to regain his honor. Despite Chuck telling them that Roark has an Intersect, Sarah and Casey refuse to help him find it without proof. Casey gets a shock of his own when he finds out that his Ty Bennett , who taught him everything he knows, is now one of the most wanted rogue agents. Suspicious of Casey's involvement in Chuck's disappearance, Devon breaks into his home.
Morgan, not knowing how close to death he just came, is hurt by Chuck's actions. To Morgan's dismay, Big Mike's internet date turns out to be his mother. Chuck goes alone and on the way, he is aided by his father, who turns out to be Orion. To make sure everything goes smoothly, she tells Morgan that he cannot come to dinner this year. While on the search for Bennett, it becomes clear that Casey may be too emotionally involved to continue with the mission.
Though broken up with Sarah, Chuck becomes jealous after noting Sarah's interest in Cole. Meanwhile, Big Mike is introduced to internet dating by Morgan, Lester and Jeff at the Buy More. 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. Chuck tries to explain his unusual behavior to Ellie and to the quirky Buy More efficiency expert Emmett Milbarge , but a new assignment only complicates things. He willingly agrees to bring down the woman who betrayed him twice. Heeding Bryce's warning, Chuck destroys the Intersect but not before downloading it into his head. Casey escapes and incapacitates the Fulcrum agents, saving Chuck and Sarah.
When the team goes to retrieve the computer Orion sent to Chuck, they run into a Fulcrum agent named Vincent. In the end of the episode, the Cipher is revealed to be implanted with a virus by Fulcrum, and exploded when activated. Morgan tries to talk Anna out of moving in with him after previously agreeing to move in with Chuck, but later decides that living with Anna is what he truly wants. Chuck foils a plot to kill the Chinese ambassador and Anna and Morgan reconcile. Steve is captured by Fulcrum, who wants him to finish building Roark's Intersect. Chuck, Cole and Sarah are captured by Fulcrum when they attempt to use Cole to lure Fulcrum. As a test, the Fulcrum agents upload their entire Intersect to Chuck's brain.
Later, Tyler convinces Chuck to go out on the town, which only leads to a night of trouble. After accidentally obtaining a part of Fulcrum's Intersect data, Chuck discovers that the suburban development is a front for Fulcrum. At the Buy More, Emmett reinstates the employee of the month contest, but Morgan, Jeff and Lester have other plans. Jill and Chuck pose as an engaged couple at her parents' home to meet her Fulcrum recruiter Uncle Bernie. Meanwhile, Devon's parents Honey and Woody make a surprise visit to help Ellie and Devon plan their wedding.
Led by Mitt , these bullies are the employees of a neighboring sporting goods store, and they love to take over Buy More's home theater room to play sports video games. The team is captured by their neighbors including Brad and Sylvia , who turn out to be Fulcrum agents. Chuck uses his government pay to give Ellie the beach-side wedding she has always wanted, allowing her and Devon to finally wed. They try to use Roark's Intersect to erase the original Intersect from Chuck, but fail. Devon offers to help Morgan pay for the apartment, but Morgan loses focus on his new grown-up responsibilities by purchasing a 1981. Chuck receives his degree from Stanford after Sarah and Casey use his field experience to supply the remaining needed credits. After finishing the game and recovering the launch codes, he phones Sarah with the information and the terrorist missiles are stopped.