A waking coma was a name used by Doctor William Glass and the rest of the staff at Oregon Memorial Psychiatric Hospital for a condition that Billy Miles suffered from, following an automobile accident on State Road in which Peggy O'Dell was also involved.
In March 1992, Dr. Glass explained to visiting FBI Special Agents Fox Mulder and Dana Scully that the condition meant that, functionally, Billy's brain waves were flat and he was persistent vegetative. Apparently, Billy Miles suddenly recovered from this condition later that month, however. (TXF: "Pilot")