Carter has described "Gethsemane" as a "big ideas episode", noting that its main concern is debating "the existence of God". The title of the episode is an allusion to the biblical garden of Gethsemane where Jesus was betrayed by Judas Iscariot. The character Michael Kritschgau was named after a former drama teacher of Gillian Anderson. The tagline for this episode is "Believe the lie", changed from the usual "The truth is out there". This episode marks the first appearance of one of Scully's brothers since a flashback in the season two episode "One Breath". Section Chief Scott Blevins makes his first appearance since the fourth episode of the first season, "Conduit".