"Biology 101": Annie and the study group welcome Pierce back much to Jeff's chagrin.
"Geography of Global Conflict": Annie must deal with a scholastic rival named Annie Kim.
"Competitive Ecology": Annie has second thoughts about teaming up with Jeff as lab partners for Biology.
"Remedial Chaos Theory": Annie and Jeff share a few intimate moments in various "timelines". In the "Prime timeline", Abed invites Annie to move into his and Troy's apartment.
"Horror Fiction in Seven Spooky Steps": Annie tells the group a story about a selfish vampire and a seemingly innocent school teacher with a dark secret.
"Studies in Modern Movement": Annie moves in with troy and Abed in their apartment but finds their juvenile antics maybe too much for her to deal with.
"Documentary Filmmaking: Redux": When the school board decrees that Greendale needs a new television commercial, Annie becomes the script supervisor under the director of the shoot, Dean Pelton.
"Regional Holiday Music": Annie tries to convince Jeff to participate in the school's Glee Club Christmas pageant by putting on a private performance for him.
"Digital Exploration of Interior Design": Annie and Jeff try to track down a student named Kim whom Jeff insulted years ago.
"Pillows and Blankets": Annie provides medical aid in a makeshift clinic for the participants in the war between Abed's Pillow Fort residents and Troy's Blanket Fort denizens.
"Origins of Vampire Mythology": Annie helps Britta avoid her ex-boyfriend Blade by keeping her on lockdown at her apartment.
"Virtual Systems Analysis": Annie tries to pull Abed back into reality after he starts to lose himself inside the Dreamatorium.
"Basic Lupine Urology": Annie teams up with Jeff to prosecute Todd for the sabotage of their lab experiment.
"Course Listing Unavailable": Annie becomes disgruntled after she learns that she has to retake "Biology" and helps to incite a riot which gets the study group expelled.
"Curriculum Unavailable": Annie and the study group reminisce about Greendale while attending Abed's mandated therapy session with Dr. Heidi.
"First Chang Dynasty": As part of a plan to stop Chang's rule over Greendale, Annie sneaks onto campus disguised as a school security guard.