The Justice Department said Thursday that it would not file charges in connection with the deaths of two prisoners held in CIA custody a decade ago, closing the last active criminal investigation into the agency’s treatment of prisoners after the Sept. 11, 2001, attacks.

The decision marks the culmination of a criminal probe that took nearly five years, examined the treatment of about 100 prisoners and branched out far beyond its initial scope — but ultimately produced no charges against any CIA officer.