He was raised on Berengaria VII and seemingly had a difficult childhood. He was a member of the last generation of Terrans to be born while the Terran Empire was at its height. As a young man, he served as an officer in the Imperial Starfleet and was dismayed by the sweeping reforms enacted by Emperor Spock which ultimately had the effect of weakening the Empire to the extent that its successor state, the Terran Republic, was conquered by the Klingon-Cardassian Alliance in 2295.
As with the vast majority of his species, he was sold into slavery. He eventually ended up on Bajor where he became the property of Jaro Essa's family. As Jaro was a member of the Bajoran dissident movement which sought the withdrawal of Bajor from the Alliance, he was treated humanely and was eventually given his freedom. However, the pretense that he was Jaro's slave was maintained in order to prevent the Alliance growing suspicious.
By 2377, he was a blind and extremely frail centenarian who was confined to a hospital bed in a dissident enclave in Vekobet in the Kendra Province of Bajor which was passed off as a labour camp in which the vital metal uridium was processed by slaves for the Alliance. In reality, the slaves, who were composed of Terrans as well as Bolians and Tellarites, were agents of the dissident movement, as were their supposed Bajoran masters. Jaro, the camp's physician and one of the enclave's leaders, cared for him with Prynn's assistance.
In January of that year, Vaughn met his considerably healthier primary universe counterpart Commander Elias Vaughn, the first officer of Deep Space 9, who had travelled to the mirror universe with Captain Kira Nerys to warn the Terran Rebellion and their allies that Iliana Ghemor intended to discover the Bajoran wormhole and become the Emissary of the Prophets. Vaughn told his counterpart about his life and that he was surprised to have lived to be over 100 years old, given that the average life expectancy of Terrans was approximately 70.
Shortly afterwards, Klingon forces from the IKS Negh'Var launched an attack on Vekobet. Recognising that he would slow down Prynn and the other dissidents, he asked his counterpart to kill him. Commander Vaughn did so by shooting him with his phaser, which led to Prynn physically attacking him. He was soon taken prisoner and transported to Terok Nor, which had been recaptured by the Alliance only hours earlier. During their captivity, Jaro and his wife Winn Adami told Commander Vaughn that they understood why he had killed his counterpart and that they forgave him for doing so. However, Commander Vaughn doubted that Prynn would be as forgiving. (DS9 novel: The Soul Key)