Classes start again at Greendale Community College and the group prepares for their new Anthropology class and teacher, June Bauer. Jeff struggles with tensions with Britta and Annie after what happened at the Transfer Dance. Senor Chang enrolls as a student so that he can join the gang's study group.
Jeff runs into his old law colleague and is soon going back to his old ways of partying and expensive attire. His friends come to rescue him, some digging up dirt on Jeff's acquaintance, and some start to become corrupted by lawyers.
When Pierce's mother dies, the group helps to comfort him. After putting Jeff in the hospital, by one of her class pranks going awry, Professor Bauer takes a leave of absence and Professor Duncan attempts to take over her Anthropology class.
Greendale gets its own space simulator after the Dean discovers that their rival school, City College, is unveiling its own orbital launch simulator. The Dean makes the group clean the simulator due to an unflattering school flag design they submitted. When inside, the simulator accidentally launches, meaning it's up to the team to get it back to campus in time of the school's unveiling.
Shirley wants to make a religious film, and when she wants to get input from Abed, Shirley finds out he is already planning on making one of his own. Pierce becomes aware of his age in comparison to the rest of the group, and is recruited by another group of students closer to his age.
When some of the Greendale staff and students ingest a bio-hazardous substance, they start to develop flu-like symptoms and turn into zombies. The group will have to save the others and themselves when the Dean locks them in with the infected.
After a classroom smackdown with a group of "mean girls" led by Meghan, Britta, Shirley, and Annie bond with Abed by turning him into the ultimate "mean girl". Meanwhile, Jeff and Troy embrace a zen-like spirituality under the guidance of a groundskeeper when they come across a secret trampoline on campus.
When Annie's pen goes missing, she suspects a member of her own study group is the thief. On a mission to find the pen and solve the mystery, the group takes a self-imposed lockdown and Jeff takes the lead in conducting the search.
When Dean Pelton begins checking class schedules, he discovers that Jeff has listed a class that doesn't exist. Just when it appears Jeff will be caught in a lie, the mysterious "Professor Professorson" emerges from the shadows to confirm that Jeff has been taking his class, "Conspiracy Theories in U.S. History", at night school. When Jeff later admits to Annie that he's never seen Professor Professorson in his life, the two decide to find out who the professor really is.
When the study group convenes to celebrate Troy's birthday, they realize he is actually turning 21 and decide to hit the bars! While Jeff and Britta ingest a few too many cocktails and get silly, Shirley gets busy pulling down incriminating photos of herself that are posted at the bar.
When Abed wakes up in stop-motion animation, he takes it as a sign that he and the group must re-discover the meaning of Christmas. Meanwhile, Jeff and Britta become growingly concerned about Abed's mental health and enlist the help of Professor Duncan. The group undergoes hypnosis to explore Abed's winter wonderland and soon unravel the truth behind Abed's madness.
Annie returns from spring break to find that her crush "Rich", the Dr., has enrolled at Greendale Community College, sparking a heated debate about whether to add Rich and/or Senor Chang to the study group. Shirley's ex-husband Andre is back in the picture and Shirley has some big news for everyone.
When Annie decides to stage a production at a local middle school to spread an important message about staying away from drugs, Pierce becomes overwhelmed with the excitement of performing and decides he needs a bigger role.
When Jeff becomes concerned about "Fat Neil", a fellow Greendale student who is a bit of a loner, Abed proposes that they invite him to play a game of Dungeons and Dragons to boost his spirits and his confidence. But when Pierce discovers that he's been excluded, he forces his way into the game and takes charge, disrupting their delicate plan.
Troy and Abed compete for the attentions of the college librarian, while Britta strives to be progressive and befriends a fellow female student whom she believes is gay. Meanwhile, Jeff finds himself reluctantly hosting an impromptu party at his apartment when Professor Duncan invites himself over to watch a soccer match.
After ingesting mysterious pills Pierce believes he is dying and gives the group his final words and specially chosen gifts, little does the group know, these gifts are meant to torment them. Jeff thinks about meeting with his long lost dad, meanwhile Troy meets his idol LeVar Burton.
Greendale prepares for the Vice President's visit. Dean Pelton organizes the first student elections, putting Annie against Jeff, Leonard and Star Burns. Meanwhile, Abed develops a friendship with special agent Robin Vohlers.
Chang's plan to prove he's responsible hits a roadblock while Britta's love life takes an unusual turn.
Things don't go as planned when Jeff plans a surprise party in "Pulp Fiction" style for Abed's birthday.
As everyone settles on their spring semester electives, Troy and Britta explore the fundamentals of acting, while Abed tackles an advanced study of 1980s sitcom "Who's The Boss?" with a professor who has written a book on the topic.
As the study group gathers to assemble their 20th and final Anthropology diorama of the year, they begin reminiscing about their favorite times together - including a trip they made to a western ghost town, a last minute glee club performance, the clandestine trysts that Jeff and Britta have pulled off and the cornucopia of costumes that Dean Pelton has managed to wear over the year.
When the Anthropology class assembles for their final exam, Shirley notices a twinge, which quickly escalates into full-blown labor. As Jeff and Britta argue about how best to help, Chang is anxious to claim this "early" labor as clear evidence that it's a "Chang Baby!"
As the Greendale student body enjoys their year-end picnic, Dean Pelton announces plans for a small, quick, safe game of paintball. As the game heats up, alliances are formed - and broken - and friendships are put to the test.
As the Greendale year-end paintball extravaganza continues, the game takes a dramatic turn with new intruders arriving on the scene. The study group battles it out on various fronts and despite their arguments over strategy - they are all in agreement that they must unite to defeat the enemy.