According to Dean, Deacon once saved John's life (presumably when they were in Vietnam together), and calls in the return of that favor by asking Sam and Dean to investigate the supernatural deaths in the Green River County Detention Center where he works as a prison warden.
The fact that Deacon knows about the Winchesters' hunting habits suggests that he and John had contact after the war and Mary's death.
Throughout the episode, the viewer is unaware of Deacon's identity. it is only when it is time for the boys' escape that we find out that Deacon is the warden. Nurse Glockner attacks Deacon but she is banished as the boys salt and burn her corpse.