With its future being much in doubt after the season 2, Chuck finally got a 13 episode re-up, with an option for 6 more. NBC line up was a bit shaky after a promising Heroes began to falter, and the end of the Jay Leno Show which lead to the option of the 6 additional shows being picked up.
Not knowing for sure if the season would be extended or if the show would be ending after the original deal for season 3, episode 13 ended neatly as a possible season or series finale. Leading up to this, Chuck gets his final test for becoming an official spy, John Casey is no longer a spy, Morgan is now a spy (or so he thinks), and Shaw finds out that Sarah is reasonable for killing his wife.
In Chuck Versus The Other Guy:
Sarah finds out that Chuck only passed his red test with the help of Casey, and that he is still the man she has loved. Shaw finds the Ring’s headquarters and takes Sarah and Chuck to take down their leader. Not knowing that they are being double crossed, Shaw is now working both sides, and takes Sarah to France to follow a lead. With the help of Morgan, Chuck goes to France to once again save Sarah. John Casey agrees to help and in doing so is able to get reinstated, Morgan gets to be a spy, and Chuck gets the girl.
The final six episodes leaves Chuck dealing with the Intersect giving him problems with his head, and dealing with his family knowing he’s a spy. His father stuck between helping his family and saving himself gets taken by the Ring. We also find out a little more about John Casey.
In a two part season finale we have Chuck Versus the Subway:
Chuck’s dad, played by Scott Bakula, works on a governor to help control the Intersect 2.0 that throughout these 6 episodes makes him think that Shaw is still alive. General Beckman has to testify in front of her superiors in order to keep Project Bartowski running. Shaw, back from the dead, still a double agent testifies for shutting down the Intersect Project.
Sarah and Casey are being held by Shaw, while the Bartowski family comes to save them. Chuck and his dad find the Ring’s Intersect where Shaw and his team capture Chuck and kill his father. Now Ellie, Captain Awesome, and Morgan are their only hope.
And Chuck Versus the Ring Part 2:
Now it’s time to take down Shaw, and take down the Ring. The team infiltrates the Joints Security Summit where the Ring Elders are captured and Shaw is exposed. Without the governor, Chuck is unable to stop Shaw as he escapes, and Intersect continues to get worse.
The Buy More gets the call that the store is closing, Jeffster and Big Mike orchestrate an unauthorized store wide sale, slashing the prices.
Shaw wires the Buy More with C4, the fire alarm is pulled to get the customers out, Chuck shows up for a Intersect vs. Intersect battle against Shaw as Jeffster’s music video rings throughout the store. As Chuck overloads, his brain is able to reboot, and defeats Shaw.
Morgan drops the detonator and the Buy More blows up, but Jeffster is the main suspect in the arson case. Chuck keeps his promise to his sister about getting out of the spy business, but after getting a message to go to his computer he gets a video of his dad, he may not be able to keep his promise. Chuck goes back to their old house and finds some information about their family, and find that their mother is still alive.
The new season finale leaves the door open for the expected return of the series for its 4th season.
Update: Not much doubt after the moderate success of the third installment, Chuck was quickly renewed for its fourth season.