Why did Jonathan leave 30 Rock? The show sneaked the answer into a joke

Nobody except Jack, once, in a line most people missed.

What really happened

Pancholy left because NBC gave him a bigger job on another NBC show. He was cast as Neal, a series regular on the sitcom Whitney, which premiered in fall 2011 and shot on a schedule that ruled out returning to 30 Rock. Jonathan was written out of season six entirely, with no in-story explanation.

The joke

In "The Ballad of Kenneth Parcell" — season six, episode four, aired January 26, 2012 — Jack is pressuring Liz to promote TGS and explains how valuable Jenna has become to the network:

"She's bigger than Maulik Pancholy on Whitney."

Which means that inside the world of 30 Rock, Maulik Pancholy exists as a separate person from Jonathan, and is a rising NBC star. The show pulled the same trick with Alec Baldwin, who gets name-checked by Jack in the series finale.

What Jonathan actually got up to

The character had a strange résumé for a background player:

• From Palo Alto — in season five's "Let's Stay Together," Jack asks him to fake an Indian accent as a distraction. Jonathan objects on geographic grounds.
• The Christmas gift — Jack once secured the release of Jonathan's sister from a North Korean prison.
• The wedding dress — Liz catches him wearing one, dancing with one of Jack's suits.
• Loyalty beyond reason — he keeps his post under Kathy Geiss and follows Jack upstairs to Kabletown.

Did he come back?

He did. Whitney was renewed for a second season, Pancholy left it, and Deadline reported in 2012 that he'd return as Jonathan for 30 Rock's final 13-episode run. He's back in season seven, including the two-part finale, "Hogcock!" and "Last Lunch."

Whitney lasted two seasons and 38 episodes. 30 Rock got seven seasons and 138. The joke about Pancholy's stardom aged into something closer to a documentary.