Critical reception to the episode was largely positive. "The A.V. Club" reviewer Zack Handlen gave "The Red and the Black" an A–, and wrote positively of the "galactic war" between the colonists and the rebels that is referenced in the episode, noting that it marked the point where "shit is about to get real". Despite this, Handlen criticized the series for not following through on its tale of alien war, noting that the premise "never really off--at least […] I've never heard anyone refer to last seasons of the show as 'the seasons when "The X-Files" mythology finally paid off.'" Handlen, however noted that "The Red and the Black" worked because "the performances are great as always, and because the second part of this two parter rarely feels bogged down or draggy." Robert Shearman and Lars Pearson, in their book "Wanting to Believe: A Critical Guide to The X-Files, Millennium & The Lone Gunmen", rated the episode three stars out of five. The two called the episode a "typical mythology runaround" and noted that the plot was "complicated but the simpler scenes of confrontation are very well handled." Paula Vitaris from "Cinefantastique" gave the episode a positive review and awarded it three stars out of four. Vitaris praised the episode's premise and wrote that it represented "a second half of a two-parter that is as strong as the first half."