"Biology 101": After Jeff is monkey gassed, he offends Shirley (and others) when he mistakes a prisoner in a picture that Pierce gave their Biology Professor Marshall Kane for Kane. He then makes it much worse when he says that he doesn’t mean that all black people are in prison.
“Geography of Global Conflict”: Jeff and Shirley are members of Annie’s Model UN team representing Uruguay and China respectively.
“Remedial Chaos Theory”: When Jeff rolls a “4” on the die, Shirley goes to get the pizzas. He tells the others not to eat the pies as baking shouldn’t be her identity in the group. This results in her pies burning and Jeff telling her they weren’t going to eat them. Shirley ends up crying and storming out of Troy and Abed’s apartment.
“Horror Fiction in Seven Spooky Steps”: In Shirley’s ghost story, she sees Jeff (and the rest of the Study Group) as doomed when the rapture comes.
“Studies in Modern Movement”: Shirley helps sing “Kiss From a Rose” to Jeff, revealing that the Study Group knows about him singing it with Dean Pelton.
"Foosball and Nocturnal Vigilantism": Shirley teaches Jeff how to beat The Germans at foosball which reveals a painful shared history they have. Once resolved, they become good friends.
"Urban Matrimony and the Sandwich Arts": Shirley asks Jeff to give the toast at her re-marriage ceremony to Andre.
"Contemporary Impressionists": While high on anti-anxiety medication, Jeff has a narcissistic Hulk-like rampage and kisses Shirley.
"Origins of Vampire Mythology": Shirley accompanies Jeff to a carnival at Greendale (pretending to be his significant other) in order to figure out why a carnie has such a hold on Britta.
"Virtual Systems Analysis": Jeff asks Shirley how her lunch at the fast food place across town went. Shirley realized it's the same fast food in a different location, so she went to the mall and had pizza.
"Curriculum Unavailable": Since Shirley's kids ate cookies meant for the Study Group, she gives some of their toys and trophies to the group. She gives Jeff a Tuskegee airman action figure.
"Digital Estate Planning": When Jeff gives a speech about not dying in the "Journey to the Center of Hawkthorne" game, Shirley sarcastically says that she used to love dying but Jeff's speech turned her around on the subject.
"The First Chang Dynasty": When Jeff is explaining the plan to break into Greendale using a diorama, Shirley complains that the figure representing her is a pine cone.
"Introduction to Finality": During the summer, Shirley asks Jeff to represent her in "Greendale Court" in her case against Pierce over their partnership in Shirley's Sandwiches. When their legal opponent turns out to be Alan Connor, Shirley's selflessness inspires one of the best Winger speeches and so impresses Pierce that he fires Alan. Shirley and Pierce agree to have Jeff be the legal owner of Shirley's Sandwiches.