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 (Prophet 5). APO quickly realized that Dean was a rogue agent (...1...).
When Dean sends two of his 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 (Prophet 5). Afterward, Rachel turns on The Shed and Dean. At the behest of APO and Sydney Bristow, she stole data from Dean's personal servers. When he discovered what she was doing, Dean destroyed The Shed's office, killing all the operatives inside - except Peyton and Gibson.
Peyton and Dean set out to rebuild their destroyed offices (Mockingbird). Marshall had been monitoring all of Dean's accounts (based on Rachel's Intel) and was noticed that Dean had liquidated everything - it was all stored in one account. This was his "fail safe." Since Rachel helped set it up, she can get in to it with the answers to his protocol questions. Sydney and Rachel get into his Prague office and retrieve the answers, then proceed to clean out his account. Following the destruction of the Shed, Dean kidnaps Sydney on her way home from a mission. He trapped her inside her car, hundreds of feet above ground by a magnetic shipping crane. He called Sydney, demanding that "Mockingbird" be returned to him.
In an attempt to destroy APO, Dean offered to arrange for Sloane's release from custody and reinstatement inside APO (Out Of The Box). He threatened the son of a Senator to manipulate Sloane's hearings. He then tasked Sloane with being his mole inside APO. In order to find Rachel's family (in witness protection), he told Sloane to find Janos Vak, a Hungarian weapons designer, using APO resources (Solo). When Sloane failed to deliver, he tasked Peyton instead - telling her to kill Rachel, if they cross paths. Peyton was unsuccessful in both jobs. When Sloane and Dean later met, Sloane refused to cooperate since they had tried to assassinate an APO agent. Dean tried to use a cure for Nadia to entice Sloane's cooperation.
Instead, Sloane went to Jack and told him everything (Fait Accompli). They agreed to use Vak to trap Dean. Later, when Dean became suspicious and took Sloane hostage, Rachel knocked him out with a shovel. In custody, he was visited by Sloane who forced him to swallow a cyanide pill so that he could not disclose the details that Sloane had not told APO. Sydney later discovered his corpse; she was suspicious, but Jack assumed it was suicide.