Despite his being between six and seven hundred years old judging by the number of tails he has, the majority of Mystery's past is still, well, mysterious. Current events imply that he fled Japan to escape from Shiromori, as he is terrified by the knowledge that she's tracking him and possibly very close to finding him now. It's not known how long ago that was, as it could be just before he became a member of the Mystery Skulls or much earlier in his life. It's also not known exactly why.

He eventually met up with Vivi, a girl with a penchant for the supernatural, and was adopted as her dog. It's most likely through her that he also befriended Lewis and then Arthur, before they all became the Mystery Skulls. He has not told any of them about his true nature yet, acting only as Vivi's pet and the group's mascot, as well as a full member of the paranormal investigation team.

Things had started out pretty well for the Mystery Skulls, they were on the road investigating places and Vivi and Lewis were a happy couple. That was until they went to investigate an old cave. Right away, Mystery sensed that something was wrong. The green mist that was everywhere wasn't the only thing that gave him that feeling and when the group split up to investigate, he secretly followed Arthur and Lewis when he was supposed to be with Vivi. From the shadows he saw something possess Arthur through his left arm and force him to push Lewis to his death. Unable to save Lewis, Mystery transformed and tore off Arthur's left arm to prevent him from being fully possessed and left it behind.

Things returned mostly to normal, as much as they could be when neither Vivi nor Arthur remembered the night in the cave clearly. Vivi actually didn't seem to remember that they were now missing a member. Arthur had made himself a new arm and they were on the road again. Until one night the van broke down in front of an old mansion. With nothing to do, they ventured inside where they found it was haunted. Fleeing further into the mansion, they were attacked by a suit of armor and Mystery nearly lost his head. Some haunted paintings then scared them onto a trapdoor, and as they fell, Mystery noticed a mirror behind him that shattered when he looked at it. He and Vivi were separated from Arthur and found the kitchen, at which point they stopped to eat sandwiches. Arthur ran by before they could eat though, and the pair soon followed when they saw the skull-faced ghost chasing him.

As the chase went on, Mystery soon found himself in front of a portrait that played back the night in the cave for him. It's likely that he realized then that the ghost was Lewis and he was only after Arthur for killing him. This would make him the only one who knows. He caught up with his friends as Arthur was pulling Vivi away from the ghost and they ran for the exit, barely escaping the explosion of ghost fire that was sent at them. They piled into the van and sped off, the mansion fading away as they escaped.

A few nights later found them sleeping on the side of the road. Mystery woke up to find Arthur on his laptop, looking at a picture of the group at Lewis' family restaurant. Only Lewis was fading away. This upset Mysery and he transformed, looking over the picture while ignoring Arthur. That is until he noticed Arthur terrified and watching him. Abruptly, Arthur jolted awake, throwing his laptop and falling out of the van when it hit him on the head. Vivi woke up and questioned what was going on which prompted Mystery, now back in dog form, to play innocent despite being wide awake. So it's likely that he put Arthur to sleep to protect his identity.

As Vivi went back to sleep, a lotus blossom's petal blew into the van and landed in front of Mystery. He picked it up, but almost immediately realized that the petal meant the Shiromori was tracking him.