In a retrospective of the first season, "Entertainment Weekly" gave "Beyond the Sea" an A+, noting how it humanizes Scully and praising the casting of Dourif. Zack Handlen of "The A.V. Club" graded the episode a B+, praising Dourif as Boggs but wondered specifically about his intentions. Despite liking the fact that Scully was the focus of the episode and praising Anderson's performance, he thought that its "main flaw" was the way it handled her moral crisis, opining that she appeared too weak.