The Phantom seems to be following Shaggy and Scooby or they conveniently wind up in all the same places as the Phantom. Fred, Daphne, and Velma do not encounter him until the finale, aside from hearing his voice through the loudspeakers.
The Phantom resembles KISS, who were later written into the Scoobyverse in A Scooby Doo Halloween (2003) and Scooby-Doo! And Kiss: Rock and Roll Mystery (2015).