Under the guise of a CIA agent working for the Office of Special Investigations, he infilitrated APO claiming to be investigating the true loyalities of Michael Vaughn. however, APO quickly determined that Dean was a rogue agent. He had faked his death two years earlier and had since then been living "off the grid."
When Shed operative Rachel Gibson learned the Shed's actual affiliation, she turned on it and at the behest of APO and Sydney Bristow stole the data from the Shed's servers. When Dean discovered what she was doing he destroyed the Shed, killing everyone except Peyton and Gibson.
Following the destruction of the Shed, Dean and Peyton undertook a series of attempts to recover or kill Gibson, with no success. Dean was instrumental in securing the release of Arvin Sloane from federal custody and getting Sloane's security clearance reinstated so that Sloane could work for Dean inside APO. He also had some undetermined connection to Sloane prior to this.
Dean was captured by Gibson and taken into APO custody. While in custody he was murdered by Sloane at the request of Peyton, but also to cover tracks indicating that Sloane had been disloyal to APO.