Dixon eventually learned the truth about SD-6 after Sydney's latest mission resulted in them acquiring access to the Alliance server, including the access codes to all twelve SD bases; needing to confirm that the current codes were valid, but with Jack Bristow exposed and captured while Sydney's cover was compromised, she was forced to tell Dixon the truth as the only other agent in SD-6 that she could trust.

Following the downfall of SD-6 and his resentment at Sydney for not apparently trusting him, Dixon was pressured by his wife Diane who was now angered by the many years of lies from her husband.

However, he initially finds that he does not wish to make her worry about him coming home at night, and decides to request at transfer to intelligence, which would mean a desk job in analysis.

Dixon's two children, Robin and Steven, were once kidnapped by The Covenant in an attempt to forcefully extract an artifact created by eccentric 15th century inventor, Milo Rambaldi.

At the start of the fourth season, Dixon had stepped down as director and resumed duties as a field agent alongside Sydney in the new Authorized Personnel Only (APO) black ops division of the CIA.

In the series finale, a flash forward several years into the future reveals that Dixon has again taken a promotion to the position of Deputy Director (although it is not explicitly stated that APO still exists).