While having a terrible day, Dr. Cox destroys Franklyn's lab in a fit of rage. He pays for the damages later when he is in a better mood. ("My Heavy Meddle"). Later that year, when J.D. is trying to find an error in Ben Sullivan's paperwork, he asks Franklyn, who claims to be too busy to help. J.D. asks Elliot to cry in front of Franklyn, who then decides to help. ("My Occurrence")
The next year, Janitor uses a crossword puzzle to trick J.D. into saying an offensive racial slur about Asians with Franklyn around. ("My T.C.W.")
When Elliot feels discriminated around Sacred Heart for being a woman, she tries flirting with Franklyn to get him to process her patient's urine samples first. ("My Unicorn")
A special microscope that he protects from Dr. Cox.
Franklyn is also arguably one of the miscellaneous characters who should have appeared in My Finale. However, Masi Oka (along with Sarah Lancaster who plays Lisa/"Gift-Shop Girl") was denied permission by NBC to make the appearance.