Ghostfreak was rarely used by Ben because when he was used, Ben did horribly violent actions that made him fear Ghostfreak.
Eventually, this was revealed to be Zs'Skayr, who escaped from the Omnitrix and tried to take over Ben's body for the device to access his full form. This failed, but he got his hands on a Forever Knight's copied Omnitrix and used that to return to his normal state after possessing the body of a news reporter.
He died in a massive battle but was brought back to face Ben and the Plumbers by a team made up of Null Void convicts.
Over time, he would meet the group on a few more occasions before being scanned by the Omnitrix. His soul would die but his form would be accessible by Ben from that point onward.
Identical to the original Ghostfreak. He gains a green eye by Volume 5 by having all his dark side erased.
Behind the Scenes
To the writers, they had a strong feel of what they wanted to do with Ghostfreak and Zs'Skayr. Unfortunately, this fell apart post-Volume 2 so they just decided to give him back to Ben.