Why did JJ leave Criminal Minds? The real reason had nothing to do with the story
When JJ told the BAU she was taking a Pentagon job in season 6, it felt abrupt — because it was. The storyline was written in a hurry to cover a decision made in a CBS boardroom, and actress A.J. Cook had no say in it whatsoever.
She was fired — over money
In June 2010, CBS declined to renew Cook's contract ahead of season 6, in what was widely reported as a cost-cutting move. The network cut her loose entirely and, at the same time, reduced Paget Brewster (Emily Prentiss) to a smaller episode count for the season. Two of the show's three main female leads, gutted in one swoop.
Cook broke the news to fans herself on Twitter in June 2010:
"So it 's true. I'm officially not returning to Criminal Minds."
She was brought back for just two episodes at the start of season 6 to write JJ out. Her farewell episode — fittingly titled "JJ" — aired on September 29, 2010, with the character transferred to a Department of Defense job at the Pentagon.
The backlash was immediate
Fans revolted. Petitions gathered tens of thousands of signatures, cast members publicly criticized the decision, and critics called out the optics of a crime show cutting its women while every male lead stayed put. CBS spent the entire season on the defensive.
How she came back
By 2011, CBS reversed course completely. Cook returned in the season 6 finale and was back as a full-time series regular from season 7 onward — with JJ upgraded from media liaison to full profiler. She stayed for the rest of the original run, which ended after 15 seasons in February 2020, and returned again for Criminal Minds: Evolution, the Paramount+ revival that launched in 2022.

In the end, the woman fired for budget reasons became one of the longest-serving cast members in the franchise 's history.
So the Pentagon storyline was pure cover?
Completely. There was no creative plan to move JJ on — the writers built the Pentagon exit around a contract decision, then quietly built the return the moment the contract came back. If the exit episode felt like the show was apologizing to the character in real time, that's because it more or less was.
For the record: JJ's season 14 confession of feelings for Reid caused more fan chaos than her firing ever did.
Some exits you can undo. Some plotlines, apparently, you can't.