As the cast and crew of TGS with Tracy Jordan returns for a new season, Liz is excited to see Jack again. However, her excitement quickly fades as Jack insists that Liz is still not over Floyd. Meanwhile, Jerry Seinfeld shows up at Jack's office in an upset mood after Jack announces his newest plan. Finally, Kenneth becomes Tracy's office wife when Tracy separates from his wife and Jenna returns to set a whole lot heavier now that she has been involved in Mystic Pizza: The Musical!.

When Jack discovers that his boss is retiring, he decides to get in the competition for his position. Meanwhile, Jenna begins to enjoy her fame for being fat and along with Jack encourages Liz to get her act together. Finally, Kenneth makes it his mission to get Tracy and Angie back together.

Jack hires his own private investigator to lead GE in the wrong direction so that they will not be able to find any dirt on him that might put him in a compromising position. However, when he is asked to give up his cookie jar collection, Jack finds the task too much of a challenge. Meanwhile, Angie announces that she will follow Tracy at all times to keep him in line, which Liz believes to be good until she covers for Tracy and gets on Angie's bad side. Finally, Jenna starts to worry once she starts to lose all the weight she gained over the summer and her popularity begins to hang on the line.

Liz meets her longtime idol, Rosemary Howard, and invites her to be a guest writer on "TGS with Tracy Jordan". However, Rosemary's ideas turn out to be too much for the show, prompting Jack to pressure Liz into firing her. Meanwhile, Jack takes Tracy to a therapist to explain to him why he must do the opposite of what he is told, and Jenna ruins Kenneth's page jacket, causing him to compete in a page-off to keep his job.

It's time for Kenneth's annual house party, but he may be the only one excited about it. The soiree has only been attended by Liz in the past, so in order to get a better turnout Tracy spreads rumors that ultimately get out of hand. Meanwhile, Jack deals with NBC's new environmentally-friendly mascot, whose new-found stardom goes to his head.

Jack falls for a congresswoman he meets at a cocktail party and despite the fact that they hold opposite views, the couple agrees to put politics aside and have a secret affair. Meanwhile, Liz believes her Middle Eastern neighbor to be a terrorist and tips off Homeland Security, creating a big mess.

As part of his community service, Tracy must coach a little league team. All goes well until Jack takes interest in the team and turmoil starts from there. Meanwhile, Liz is asked out on a date by Jamie, the new coffee boy, who thinks Liz is actually younger than she truly is.

C.C. and Jack face a block in their relationship when C.C. decides to go public about the affair but Jack refuses. Meanwhile, Liz struggles to keep both Tracy and Jenna happy when the two find it hard to share the spotlight, while Frank makes fun of Toofer's Harvard education with bizarre results.

Jack gets attached to Liz's nurturing parents because they provide the love and support he never got from his mom. The staffers get ready for their raunchy holiday party, but Kenneth changes their plans at the last minute.

Jack and C.C. try to make their long distance romance work, Liz decides to invest in real estate, and Kenneth becomes addicted to caffeine.

When someone on the 'TGS with Tracy Jordan' staff insults Jack in a newspaper article about the season finale of 'MILF Island', he frantically sends Jonathan to interrogate everyone on 'TGS' until the culprit is found.

Dennis becomes a New York City celebrity after jumping in front of a train and saving someone who fell on the tracks. Meanwhile, Jack desperately tries to persuade Tracy to become the celebrity face of the Republican Party.

When Don decides to promote Jack and make him his successor over Devon, Jack decides to give his old job to Liz because she always has his back. However, a turn of events concerning Don's health compromises Jack's promotion. Meanwhile, Tracy thinks that his son is embarrassed of his career because he did not invite him to fathers day at school.

In the second season finale, Jack moves on to a new job involving politics in Washington, but the position is not quite what he anticipated. Meanwhile, Liz suffers a pregnancy scare, Kenneth confronts rival page Donny when applying for a summer job, and Tracy works on his latest invention.