"Beyond the Sea" was written by "The X-Files" co-executive producers and long-time writing partners, Glen Morgan and James Wong; it was their fourth script for the series. The episode was directed by David Nutter. As Morgan and Wong explained, their episode was written in response to criticisms of the show's initially limited characterization of Scully. Wong said, "Gillian Anderson needed to show off her talents more, and this was a perfect opportunity to dispel those notions that Scully will never believe. It was time for the character to grow, because she was just doing the same kind of thing too often." Executives at Fox vetoed the idea two times before Carter told the network, "we're doing it."