Under the guise of a CIA agent working for the Office of Special Investigations, he infiltrated APO to be investigate allegations that Michael Vaughn was a double agent (5.01) APO quickly realized that Dean was a rogue agent. He had faked his death two years earlier and had since then been living "off the grid."
When Dean sends The Shed operatives Rachel Gibson and Kelly Peyton to Istanbul to steal "Substance-33" (a deadly nerve agent), the APO team tells Rachel that Dean is actually working for the Prophet Five (5.03). Afterward, Rachel turns on The Shed and Dean. At the behest of APO and Sydney Bristow, she stole data from the Dean's personal servers. When he discovered what she was doing, Dean destroyed The Shed office, killing all the operatives inside - 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.