Now working for the Federal Bureau of Investigation with agent Emma Hollis (Klea Scott), Black seeks to discredit and expose the Group for their sinister motives.

Henriksen was nominated for a Golden Globe Award for Best Actor in a Television Drama, losing out to Dylan McDermott's portrayal of Bobby Donnell in The Practice.

Uhlich described the season as "a divisive run of episodes that, for many viewers, blasphemously rewrites what came before",[13] but favourably compared it to the fiction works of Jorge Luis Borges.

[13] DVD Talk's Randy Miller also awarded the season an overall four out of five stars, finding that although its concern about the then-coming millennium made it very much a product of its time, it did not seem to have suffered from this and held up well in retrospect.

Miller considered Henriksen's portrayal of Frank Black to have been "masterful"; however, he felt that the retcon of its second season finale alienated viewers and led to its dwindling popularity.

[14] Robert Shearman and Lars Pearson, in their book Wanting to Believe: A Critical Guide to The X-Files, Millennium & The Lone Gunmen, rated several episodes across the season highly, awarding five stars out of five to "Borrowed Time", "Collateral Damage", "Darwin's Eye" and the series finale "Goodbye to All That".

However, several episodes also fared poorly in their opinion, including "Closure", "...Thirteen Years Later" and "Forcing the End", all of which the pair rated only one star out of five.

Club, Zack Handlen described the season as suffering from several problems, specifically mentioning "its lack of a center, its hamfisted morbidity, the ongoing blahtastrophe that is [Emma Hollis]".