This is the only episode of the series to have been directed by regular Star Trek director Winrich Kolbe and was the final Star Trek episode directed by him.
Writer André Bormanis conceived of the insidious and enigmatic aliens because he figured that during early space exploration, humans would surely encounter species so different from other humanoids that they could neither understand nor communicate with them. He originally considered making them Romulans, who would be kept off-screen since the first visual contact between humans and Romulans chronologically doesn't take place until a century later, in Balance of Terror (1966). However, it was decided to make them a different species, as their ships were felt to be too sophisticated for 22nd century Romulans (who would be featured in season 2's Minefield (2002)). New aliens were designed by Dan Curry and represented with CGI models built by John Teska. No name was given in the script, so several members of the art department referred to them as "Shroomies" due to their mushroom-shaped heads. Star Trek Online later unofficially named them the "Elachi".
When Captain Archer is using the visual sensor array to communicate with the aliens, the sound effects engineers used a modulation device called a Flanger to create the swirling effect of Archer's voice.
Mark Latrelle's contention that Reed dislikes fish is later disproved by a scene in Shuttlepod One (2002), in which Reed's first choice of emergency ration is sea bass.
The mysterious ship that attacks Enterprise in this episode is of the same configuration as the numerous Kovaalan ships that later attack Enterprise in a subspace corridor in E² (2004). However, these similarities are probably unintentional, a result of the digital ship model for 'Silent Enemy' being recycled for 'E²', a frequently used cost-saving measure on the show. Nevertheless, the Star Trek Encyclopedia lists the ship from this episode of potentially Kovaalan origin, even though this may not have been the writers' intention.