As an advanced trainee at the Psi Corps Academy, Stoner was assigned to oversee the development of Talia Winters, a first year cadet. The two hit it off with Talia finding Matt to be charming, sympathetic and, at first, made the difficult P5 Psi Corps training easier for her to deal with. Shortly after the Corps decided that the pair would be genetically compatible and likely to produce children of equal or greater ability, the pair were married. For Talia, however, it wasn't long before she realized the union was a mistake and it would cause some difficulty. The Psi Corps annulled the marriage when Matthew later "lost" his telepathy and "officially" released him from the Corps. In actuality his telepathy had been transformed, making him a strong projective empath.
Stoner would spend the next several years working as a freelance navigator and part-time trader. In 2259 he participated in an archaeological dig at an abandoned Centauri colony in Sector 127 before travelling to Babylon 5. One of the artifacts recovered from that dig was a statuette booby-trapped by Narns, which would fire a poison dart when touched by a Centauri. This statuette was sold by Stoner to a merchant in Babylon 5's Bazaar and then purchased by Mariel, who used it in an assassination attempt against her husband Ambassador Londo Mollari. Although Stoner claimed that the involvement of his merchandise in the ambassador's near-fatal incident was a coincidence, he was in fact an old associate of Mariel and conspired with her.
Stoner's main business on the station was to get his ex-wife Talia Winters, resident commercial telepath, to come with him in the hopes of breeding more empaths. He claimed that he had been cured of his telepathic abilities and that he could recreate the treatment for Winters, knowing that she wanted to leave Psi Corps. His plan was foiled when Michael Garibaldi, with whom Stoner had shared an instant dislike, realized what Stoner was and what he was up to. The Psi Corps then stepped in to prevent Stoner from being detained on Babylon 5, showing that he had not really left their employ.