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Jonathan is Jack's assistant. His obsessive admiration of Jack is coupled with disdain towards Liz, whom he considers unworthy of Jack's attention. In season 4, episode 11 ("Winter Madness") it is revealed that Jonathan is of Indian descent, and in episode 18 ("Khonani") he addresses the janitor Khonani in Hindi. Elsewhere, he mentions meeting his "birth parents," revealing he is adopted, and when in the season-five episode Let's Stay Together, when Jack asks Jonathan to provide a distraction by pretending to be a stereotypical Indian and faking an Indian accent, Jonathan objects "But I'm from Palo Alto!" As a Christmas gift one year, Jack secured the release of Jonathan's sister from a North Korean prison. Jack's wife Avery was later kidnapped to North Korea herself. Liz once caught Jonathan wearing a wedding dress and dancing with one of Jack's suits. ("Hogcock!") Jonathan retains his position when Jack is replaced by Kathy Geiss, and is heartbroken by Jack's departure. He subsequently follows Jack upstairs, when the latter is appointed chairman of Kabletown and eschews the company's Philadelphia headquarters in favour of remaining in the G.E. Building. ("Hogcock!" / "Last Lunch") Jonathan is off-camera throughout the show's sixth season, something that the characters appear not to notice. His disappearance was due to actor Pancholy's costarring role on another NBC sitcom, Whitney. Pancholy exists within the 30 Rock universe independently of Jonathan, being mentioned by Jack in "The Ballad of Kenneth Parcell" during that period; Alec Baldwin likewise exists independently of Jack who mentions the actor in "Hogcock!". Jonathan is once again seen in season seven.

It appears that Jonathan is in love with Jack, similar to Waylon Smithers and Mr. Burns' relationship in The Simpsons. When Liz Lemon said Jack was a "bit of a stress eater" in "The Baby Show," Jonathan was very defensive of him, saying "he puts up with so much," presumably referring to Jack's overbearing mother.

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