Back when he was known as Aldous Witch, he was once an instructor at Hero Factory, teaching rookie Heroes about astronomy and architectural geology. Aldous Witch had always desired the Hero Core that Heroes wore on their chest. He then tried to supercharge himself in the Quaza Recharge Chamber only to be stopped by Preston Stormer. Mr. Makuro then banished Aldous Witch from the Hero Factory for his actions. He then traveled to the jungle planet of Quatros, using the Hero disarm passwords to disable the force shields (around the planet), and began illegally mining for the dangerous mineral himself. He found himself in danger due to the planets animals, and sent a distress call to Hero Factory, though he later escaped to safety. While excavating, he wandered into an ancient temple which housed a stone skull and fashioned it onto a staff he found. When he added a sliver of Quaza, the staff not only amplified the power of the Quaza, but transformed him into the Witch Doctor. The Witch Doctor then started to enslave the planets wildlife by outfitting each of them with Quaza Spikes and ordering them to mine for Quaza. The Alpha 1 Team responded to his earlier distress call, after getting a report from Rocka. The Witch Doctor confronted the heroes himself and revealed his true intentions to them. Furno attempted to strike him, but the Witch Doctor pushed him back. He revealed that the Quaza made him powerful and with their ship, he could escape once he took the last of the Quaza and warped away and sent corrupted wildlife after the heroes, and began to battle them. The Witch Doctor was yet again confronted by the heroes when Rocka used a warp device to reach his airship. The Witch Doctor sent his animals at them again and engaged Rocka XL in combat. During the fight, Stormer stole his staff and Rocka easily defeated him. When the heroes noticed Witch Doctor's actions were destroying the planet, Furno quickly destroyed the Witch Doctor's airship and released the Quaza into the planet's core. The Witch Doctor was then taken to Makuhero City and imprisoned. The Witch Doctor escaped during the breakout, but was recaptured.
The Witch Doctor later returned to Equestria to steal Quaza from the mines and used his Skull Staff to hypnotize Applejack, Rarity, and Twilight to find it for him. He started with Rarity and ordered her to find him Quaza and Rarity brought him three containers of Quaza and Smokescreen, Pinkie Pie, and Bumblebee tried to get it, but Rarity repeled them. The Witch Doctor then woke her from her trance and tried to shoot her with his clawed launcher weapon, but Bumblebee saved her. He then went to find more Quaza and encountered Rainbow Dash, Arcee, Applejack, and Bulkhead. He locked Arcee, Rainbow Dash, and Bulkhead in a force-field and hypnotized Applejack to find him more Quaza and sent her off to find Quaza. She managed to find Quaza and put it in a wagon and bucked it back to the Witch Doctor before being woken up from her trance by his staff. Starlight Glimmer and Twilight Sparkle then try to apprehend him, but the Witch Doctor used his Skull Staff to hypnotize Twilight to find him Quaza and Twilight went to do so. Twilight found Quaza and a Scorpio attacked her. The Witch Doctor then prepared to blow a whistle to release Twilight from her trance so she'll be a snack for the Scorpio, but Starlight grabs the whistle and uses it to free Twilight from her trance and the Witch Doctor was furious when they escaped and tried to stop them from escaping by using his Scorpio, but they manage to remove the Quaza spikes and the Scorpio turned on the Witch Doctor and helped defeat the Witch Doctor. The Witch Doctor was wounded and retreated to where he came from, vowing revenge.
He appeared in one of the alternate timelines where
The Witch Doctor later discovered a fifth Alicorn princess named Flurry Heart was born and decided to use her for his purposes