Pierce and a few other Greendale students ingest a biohazard substance at the school Halloween Party, causing them to exhibit flu-like symptoms and begin turning into zombies. It is up to the rest of the gang to save themselves and the school when Dean Pelton locks them in with the zombie-infected student body.
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. Determined to uncover the source of their new bliss, Pierce ends up taking a disastrous turn on the trampoline and lands in the hospital.
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.
When Pierce lands in the hospital, he believes he's dying and gives the study group specific gifts that are actually meant to torment them. Britta wonders what to do with a blank check for "charity," Jeff ponders the idea of meeting his father, and Troy gets to meet LeVar Burton, while Abed films the whole thing for a documentary.
The study group chooses their spring electives. Britta and Troy explore an acting class, and Abed picks a course that studies the 1980s sitcom Who's the Boss?. Meanwhile, Jeff and Pierce take a wine tasting class where they meet a mysterious woman who sweeps Pierce off his feet which raises Jeff's suspicions.
As the study group assemble their 20th and final diorama for their anthropology class, they reminisce about their favorite moments over the past year. Meanwhile, Troy's monkey reappears but disappears back into the ventilation system, leading Senor Chang to try to get the monkey and retrieve all their stolen loot.
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. When a mysterious and threatening figure emerges on the Greendale campus, it becomes apparent that this is no ordinary game of paintball.
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 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.
Jeff competes to earn the group places in the over-booked 'History of Ice Cream' class, while Abed struggles with the inevitable end of their time at Greendale, causing him to enter a 'happy place' in his mind showing bizarre alternative versions of Greendale. Annie and Shirley pull pranks around the school.
Francesca “Frankie” Dart is hired as CFO of Greendale after a roof collapses from 40 years of Frisbees. Tasked with fiscal responsibility, Frankie suggests cutting unnecessary classes such as “Ladders” amongst other changes, and Abed helps Frankie. Struggling to keep Shirley’s Sandwiches afloat, Britta, Annie, Jeff and Abed turn it into a speakeasy after Frankie bans alcohol on campus.