As the Greendale study group gathers in the library, they wonder whether they will see their old friend Pierce, who left the study group in a huff after last spring's paintball game.
Senor Chang settles in with his new job as a Greendale Campus Security Officer, while Britta is dealing with issues of civil disobedience after her friend is taken hostage in a foreign country. Annie is taking part in the Model United Nations competition and asks for help from the group to defeat her "friend" Annie Kim.
When Troy and Abed decide to share an apartment, they host a party for the group, which takes on an altered reality as several scenarios play out.
As the study group sets to work on their first big assignment in biology - a terrarium - they are driven to distraction over how they should pair off to do their project. Elsewhere on campus, Chang (Ken Jeong) patrols the school grounds looking for signs of trouble and imagines himself in a noir detective mystery.
At the group's Halloween pre-party, Britta enlists Jeff to help draw out a potential sociopath and the two of them lure everyone into telling their favorite horror stories. The results are spooky.
When Pierce learns that he and his Hawthorne wipes have become extremely popular, he decides to throw a big party, until his overbearing father, Cornelius Hawthorne shows up and puts the kibosh on the plans. Meanwhile, Troy finds himself being courted by Vice Dean Laybourne and his secretive Air Conditioning Repair Annex, as well as Greendale's resident janitor, Jerry.
The study group pitches in to help when Annie decides to move in with Troy and Abed, but the plan breaks down when she becomes frustrated by their fun-loving lifestyle. Elsewhere, Dean Pelton discovers Jeff at the mall and blackmails him into spending a lovely afternoon together.
When the school board asks Dean Pelton to make a new commercial for the school, he enlists the study group to star in his production. As he gets swept away with the project, more of the student body is pulled into the fray, including Magnitude, Fat Neil , Garrett, Leonard, Star-Burns and even Greendale alum and genuine celebrity, Luis Guzman. Meanwhile, Abed films all the activities for a documentary.
When a group of arrogant students commandeer the foosball table at school, Jeff and Shirley unite to defeat them. Meanwhile, Annie accidentally breaks Abed\'s new limited edition \"Dark Knight\" DVD and claims that someone broke into the apartment and stole it. Things snowball out of control when Abed thinks he knows who took the DVD and sets about getting it back.
When the Greendale Glee Club is unexpectedly sidelined, the school\'s effervescent choir director Cory Radison sets about recruiting the study group members to fill in. Skeptical at first, they eventually fall under his hypnotic spell - one-by-one - singing and dancing their way to the annual Christmas Pageant.
Andre proposes that he and Shirley remarry and a wedding date is set. Britta and Annie get busy planning the wedding and Jeff prepares to give a wedding speech - while Troy and Abed get ready to be "normal" for the occasion. Meanwhile, Pierce and Shirley pitch a sandwich shop idea to Dean Pelton for the Greendale cafeteria.
As the study group returns after winter break, Jeff reveals that he\'s been seeing a shrink and he\'s on anti-anxiety medication. The newfound confidence leads him to experience debilitating levels of narcissism, which Britta tries to help him manage. Meanwhile, over the break, Abed developed a celebrity impersonator habit that has saddled him with debt. In order to help Abed shed his debt, the study group dons costumes and goes to work for Vincent as celebrity impersonators - appearing in character at a Bar Mitzvah celebration.
As the new Greendale Subway shop opens in the cafeteria, Shirley, Pierce and Britta plot to bring about its early demise. Vice Dean Laybourne makes another attempt to get Troy to join the Air Conditioning Repair Annex, while Abed and Troy find themselves at odds over their competing pillow and blanket forts.
What started as a casual disagreement about blankets and pillows blossoms into all-our war on the Greendale campus. While insults are hurled and the study group chooses sides, Jeff tries desperately to negotiate a truce, but with neither Abed nor Troy budging on their principles or their real estate, the future looks grim for the former best friends.
When Britta's old flame "Blade" returns to town with the traveling carnival, she confesses to the group that she needs their help to stay away from him. While Annie, Troy and Abed scheme to keep her occupied and away from Blade, Jeff and Shirley head to the carnival to get a look at the mystery man. Meanwhile, Dean Laybourne enlists the help of Dean Pelton to convince Troy to join the Air Conditioning Repair Annex.
When the biology final exam is postponed, Jeff encourages everyone to join him for a three hour lunch, but Annie convinces Abed to let her spend some time with him in the dreamatorium instead. What starts as an innocent simulation of \"Inspector Spacetime\" becomes a more serious examination of the study group members and Annie learns a little bit about what makes Abed tick.
When Annie discovers the study group\'s yam experiment smashed to smithereens on the science lab floor, the group mobilizes to expose the criminal and save their grade. Once Abed and Troy think they have located the perpetrator, the group conducts a \"trial\", with a reluctant Professor Kane serving as judge. Jeff soon realizes, however, that the plot is thicker than anyone suspects.
As the study group comes to terms with the death of a beloved classmate, Jeff easily adjusts, while Britta acts as grief counselor to the rest, employing what she\'s learned in her psychology class. Meanwhile, Chang is on a mission to increase his policing powers at the school and when the memorial service disintegrates into a riot, he seizes the opportunity to take more control over campus security.
Abed becomes convinced that there is a conspiracy afoot and that Dean Pelton is an imposter. When Abed is apprehended sneaking around on campus, he is required to see a therapist, Dr. Heidi, or risk being sent to jail.
Pierce is summoned to Hawthorne Enterprises to discuss his inheritance with his deceased father's former right-hand man, Gilbert Lawson. The study group goes with him for moral support and must all pitch in to play the video game of their life on Pierce's behalf - or risk losing his inheritance.
With Chang in control of Greendale, the study group develops an elaborate plan to infiltrate the campus without being detected. While Chang becomes distracted planning a big birthday bash for himself, Jeff and the study group launch their sneak attack. Meanwhile, Troy enlists the help of the Air Conditioning Repair Annex to help with their break-in plan but knows he may be selling his soul to the devil.
When Shirley and Pierce have a disagreement over their sandwich shop, Jeff agrees to argue on Shirley's behalf but much to his chagrin, Pierce retains Jeff's former colleague Alan Connor and the two must square off in "Greendale Summer Fun Court". Meanwhile, Vice Dean Laybourne makes one last ditch effort to win Troy over to his Air Conditioning Repair Annex.