The CBS crime drama's sixth run concluded with the BAU team facing a financial crisis which threatened to dismantle their operation.
Messer told TV Guide: "All of those threats that were made in the finale, that there might be changes and people were going to move on, have come true to some degree [by the season seven premiere]."
The showrunner also revealed that Morgan (Shemar Moore) will be the first team member to discover that Hotch (Thomas Gibson) and JJ (AJ Cook) faked the death of Prentiss (Paget Brewster).
"You'll learn who's been where and who's been doing what," she said.
Criminal Minds star Thomas Gibson recently struck a last-minute deal to return for the show's seventh season.
It was previously reported that the Criminal Minds writing team had assembled to begin work on new episodes while still uncertain of Gibson's status.
The seventh season of Criminal Minds will air on Wednesdays at 9/8c on CBS in the fall.
> Paget Brewster returning to Criminal Minds