"Advanced Gay": Jerry next appears in the study group's third year at school repairing a machine in the cafeteria. While waiting in the chow line, Troy sees his frustration at trying to fix the broken device and offers some advice. Jerry follows his directions and when he turns the machine on it starts functioning perfectly. Impressed again with Troy's abilities, Jerry then catches up to him. He tells him that while he respects his decision to remain a student over becoming a plumber, he wanted another chance to try and convince him otherwise. He asks Troy to meet him on the third floor men's restroom tomorrow and help him unclog a toilet; if he feels nothing for the work afterwards he'll never bother him about it again. Troy reluctantly agrees hoping to put an end to the matter once and for all. The next day, the two meet up in the restroom and having successfully fixed the toilet together Troy discovers, much to his surprise, that he enjoyed the work.
After admitting this to Jerry, they are both startled by the sudden appearance of a mysterious man wearing coveralls. He compliments Troy on his repairman skills which prompts a angry reaction from Jerry who yells at the man to go away immediately. He departs amused leaving a furious Jerry and a baffled Troy who asks the janitor what that was all about. With dead seriousness, Jerry grabs Troy and tells him that certain people will want to exploit his gifts and that he should only use his abilities for good. After he agrees, Jerry asks Troy to accompany him to the second floor restroom as someone wrecked the sink by pooping in it. Later that day, Jerry is concerned about Troy's welfare and visits the Group Study Room F asking the study group if they had seen him unaware that he had been kidnapped by the Greendale Air Conditioning Repair School. He later finds Troy at the "Gay Bash" where he is repairing the air conditioning unit.
He confronts Troy telling him that he should ignore everything the school promised him as he can have those same things by being a plumber instead. Troy questions why he is so against them and Jerry says it's because they are arrogant elitists who think they are more special then everyone else. This upsets Troy who angrily tells him that he is special and doesn't want to end up a loser like Jerry. A shocked Jerry is stunned by his response and and sadly watched as Troy stormed off.
"Basic Lupine Urology": Towards the end of the semester, Jerry is seen with fellow janitor Crazy Schmidt cleaning up the Biology lab. While discussing the details of Schmidt's imaginary love life, he makes a shocking discovery. One of the Biology yam projects had been horribly smushed which ended up turning the classroom into a crime scene.