According to his colleague, Pierce, Trepkos "[occupied] that rare place among scientists where brilliance, inspiration and great luck converge." Pierce confessed that, working with Trepkos, he often felt like the composer Salieri, whose modest musical gifts only allowed him to fully appreciate Mozart's genius.
Trepkos invented the Firewalker, a robotic probe intended to explore the depths of Mt. Avalon and record scientific data about the Earth's most primal origins, which Trepkos promoted as more important even than the exploration of space.
Firewalker returned from its first exploration carrying what Trepkos mistook for a strange rock, but was actually the first known example of a silicon-based lifeform. Trepkos became so immersed in studying it that he failed to notice that, by pulverizing it, his team had become infected by it. When he realized this, he sabotaged Firewalker, destroyed all his data, and began stalking the members of his own team, ensuring that none of them could leave their compound and spread the contamination to the rest of the country.
After the last infected member of his team, Jesse O'Neill, was killed by the organism, Trepkos allowed FBI Agents Mulder and Scully to leave. Trepkos was last seen carrying O'Neill's body into the depths of a cave beneath Mount Avalon, never to return. Their bodies were never recovered, and he was presumed dead. Firewalker was recovered, though Trepkos had deliberately damaged its systems too thoroughly for any of its data to be examined. (TXF: "Firewalker")