Since Operation Double, Zygons were protected on Earth, and so Ballon posed as one in order to avoid detection by UNIT when he accidentally killed a family on Earth in self defence. He was instead captured by the Governors.
The Governors imprisoned Ballon until he came of use. With the help of the Metaphysical engine, he joined Dorothea Ames and Andrea Quill on a mission to remove the arn from Quill's brain, and became the surgeon responsible for doing so. He helped Quill get the arn pheromone that calmed the arn, the blood of the God of the Lorr to unfreeze his hands and the brain of the Quill Goddess to help him succeed at the surgery.
After Ballon was successful in removing the arn in what he thought was Coal Hill Academy, he and Quill had sex, and they conceived a child. They then encountered Dorothea, who created a hologram of Coal Hill Academy, and who told them that they were really inside the Cabinet of Souls, while also revealing that she had already left, and holographically projecting herself to talk to them.
Dorothea then tempted Quill with a new displacement gun, but warned that only one of them could escape the cabinet and that they would have to kill the other to escape, as there was only enough energy left to return a single being. Dorothea tried to tempt Ballon with the promise that they had found another Lorr, his niece, hiding somewhere on Earth. Quill and Ballon fought, Ballon gaining the upper hand and retrieving the displacement gun. He decided to use the gun to kill Quill, but the gun had been triggered to kill the user instead and it did so, firing back on Ballon.