"Anthropology 101": After Britta declaring herself the people's champion and is a hit with Greendale women for her rejection by Jeff at the previous year's "Tranny Dance", Troy apologies to Jeff and then calls him a jerk to be popular with the women.
"Accounting for Lawyers": At the "Pop and Locktober Fest", after Troy tags in for Chang, Jeff tags in for Troy and they pair up for some dance moves.
"The Psychology of Letting Go": After the Study Group learns Pierce's mom died and discuss how his Reformed Neo Buddhism religion doesn't address her death, Jeff tells them to let Pierce have his beliefs and that they should all be cool like him. Troy says Jeff ends a lot of his speeches that way. Later, Jeff takes Troy (and Pierce) for ice cream in his car.
"Basic Rocket Science": Troy takes command of The Eleven Herbs & Space Experience and tries to get Jeff to take his station. Jeff makes fun of Troy but eventually comes to respect his opinion and calls him Captain. Once the mission is over, Jeff hugs Troy and gives him a "complisult" on his ability to be a real astronaut.
"Messianic Myths and Ancient Peoples": In the end tag, Troy dresses the same as Jeff and copies what he says.
"Epidemiology": At Halloween, Jeff makes fun of Troy's "Alien" costume so Troy changes to a "sexy Dracula". Later, Troy, Jeff and Abed try to escape the students who have become zombies by running into the basement. Troy is the only one to escape and before he succumbs to the infection he says Jeff is still cool as a zombie.
"Aerodynamics of Gender": While playing basketball, Jeff and Troy discover a secret garden with a trampoline. The gardener Joshua explains the purpose of the trampoline and as they bounce, they experience incredible peace. Unfortunately, Pierce is jealous of their calm demeanors, discovers the garden and ruins it for them. Joshua is fired and they discover he is racist. Jeff feels guilty and buys Troy ice cream.
"Cooperative Calligraphy": When Annie's pen goes missing in the Study Room, Jeff locks the room down and everyone's possessions are searched. Jeff dumps Troy's backpack out but only finds a pillow. Jeff compliments Troy and says he just became his hero. Later, the group strips down to their underwear. Troy compliments Jeff's underwear and says they looks luxurious. After exhausting all options and not finding Annie's pen, Jeff supports Troy's theory that a ghost took the pen.
"Conspiracy Theories and Interior Design": As Jeff and Annie chase Professor Sean Garrity through Fluffy Town they are blocked by a Latvian Independence parade. As Jeff curses, Troy says to him that they had the proper permits and then points out Garrity to Jeff in the parade who Jeff tackles.
"Mixology Certification": When learning that Troy is turning 21, Jeff upgrades his party from cake in the Study Room to a night in a bar called "The Ballroom". Jeff and Britta try to show Troy the ropes of "adult life" but he learns that they know no more about being a grown-up than he does. Troy gets to drive Jeff's Lexus.
"Asian Population Studies": Troy goes against Jeff and votes for Rich Stephenson to join the Study Group instead of Ben Chang as Troy like Rich's kettle corn.
"Advanced Dungeons & Dragons": When starting to play D&D, Jeff introduces his character. Troy says hi to Jeff's character and then introduces his. After Jeff forges a plan to go to a town to get a Pegasus, Troy responds with "huzzah!". When Pierce reveals that Jeff coined the phrase "Fat Neil" and Jeff says he'll make it up to Neil, Troy responds with a much less enthusiastic "hazzah".
"Early 21st Century Romanticism": When Jeff insults the "Bare Naked Ladies", Troy is the first one to jump to their defense and argue with Jeff.
"Intermediate Documentary Filmmaking": When LeVar Burton shows up at Brooks Memorial Hospital to meet Troy (at Pierce's bidding), Jeff shows Burton where Troy is. Later, when Jeff attacks Pierce in the town car, Troy pulls Jeff off of Pierce.
"Intro to Political Science": Troy tries gets Jeff (and Annie) from the storeroom to watch the "political showdown of the century", that is, Magnitude and Leonard go "pop pop" and raspberry at each other.
"Competitive Wine Tasting": When Britta announces that she and Troy are taking the class "The Actor Inside" together, Jeff asks Troy how he got dragged into taking it. Troy just smiles. Jeff then asks if foosball was full, Troy says he's on the wait list.
"Paradigms of Human Memory": When Abed reveals that Jeff and Britta have been hooking up all semester, he says to Jeff that the group agreed to not have sex with each other or themselves. Jeff points out they never agreed to the "themselves" part and this makes Troy even angrier. One of the examples where Jeff put himself before the group is shown. In hair-cutting class, Jeff distracts Troy and then switches his mannequin's wig for Troy's much better one. After a Winger speech, Troy says to Jeff that it's OK if he and Britta want to keep hooking up.
"Applied Anthropology and Culinary Arts": After Troy and Abed sell their special handshake to Pierce and it doesn't feel the same when they do it, Troy goes crying to Jeff that Pierce has tainted the handshake and they can't get the magic back. Jeff points out that Shirley is having a baby two feet from them and no one cares about their handshake.