JJ was kidnapped and tortured by terrorists.
In 2010, Jennifer Jareau was reassigned to a special U.S. Military team on a mission to find Bin Laden. The intel gained from her operations were stored in a database called "Integrity," a failsafe put in place to protect covert operations and agents.
When JJ was later abducted and tortured for intel related to her previous work in Iraq, Agent Emily Prentiss returned to help the rest of the team save her. Luckily, they were able to track down the bad guys and stop the information about the covert operation from landing into the wrong hands.
(Season 9, Episode 14, "200")