Kines returned as defensive coordinator at the University of Alabama in 2003 and remained in that position until head coach Mike Shula was fired on November 27, 2006. In 2005, he was named a finalist for the Broyles Award, given annually to the nation's top college football assistant coach. Kines was named interim head coach and guided Alabama in the Independence Bowl where they lost to Oklahoma State, 34–31. New Alabama head coach Nick Saban did not retain any of Shula's staff; however, Kines was hired as an officer with Tide Pride, which is responsible for helping to fund scholarships, generating revenue for capital improvements, and supporting the "Million Dollar Band", among other activities.