The character was written out of the CBS drama during the recent sixth season, but will return as a series regular in the fall.
Messer told TV Guide that the special agent's return will cause "tension" amongst the BAU team, most of whom believe her to be dead.
"Hotch (Thomas Gibson) and JJ (A.J. Cook) kept a big secret from the team," she explained. "[But] ultimately, those kept in the dark will forgive the others when they find out Prentiss is alive."
Prentiss will "absolutely" be changed by her time spent living under an assumed identity, she added.
"No-one goes into hiding and comes out unscathed," she claimed. "She has been in defensive mode for months now. She'll be exhausted and will have to face the family to explain a few things."
Messer also hinted that the fan outcry following Paget Brewster's original departure had led to the restoration of the original Criminal Minds team.
"Their love for our show and investment in the characters is beyond encouraging," she said. "If their enthusiasm helped everyone see how important the unity of our team is, [then that's] fantastic."
Criminal Minds' seventh season will air on Wednesdays at 9/8c on CBS in the fall.