Having proven its success, The X-Files was renewed for a second season. But Chris Carter once again clashed with Fox over Jillian Anderson's casting. Anderson had become pregnant during production of Season 1 and needed time off. Fox once again insisted on another blonde bombshell type to take over the role, but Carter instead opted to integrate the pregnancy into Season 2's story arc. After briefly considering the idea of Scully giving birth to an alien, he instead devised a plot where Scully would be abducted, allowing Jillian Anderson her needed time off. Moulder is instead partnered with upstart FBI agent Alex Krycheek, played by Nicholas Lea, who had previously appeared in Season 1's Gender Bender.
The status quo shakeup facilitated by the shutdown of the X-Files creates a string of strong episodes in the first half of the season. Following another alien encounter in "Little Green Men," the show delivers more memorable monster of the week outings. "The Host" sees the agents hunt down a sewer-dwelling killer mutant, a creature feature full of tense sequences and gory action. In "Sleepless," Moulder contends with a vengeful Vietnam vet who has the power to kill with dreams, featuring Tony Todd as the illusionist killer Preacher.
In keeping with the status quo shakeup, at first Krychek appears to be a believer like Moulder. In contrast to Scully's skepticism, Krychek's open-minded views position him as a potential pupil for Moulder to mentor, only for the final scene to reveal him as a spy working for the powers behind the alien conspiracy. This uneasiness extends to the pivotal two-parter "Dwayne Barry" and "Ascension." When an alleged alien abductee takes hostages, Moulder is sent in as a negotiator, but his sympathies may be misplaced. Steve Railsback turns in an outstanding guest performance as the unhinged Dwayne Barry, creating constant tension around his character. The two-parter evolves from a suspenseful standoff to an edge-of-the-seat manhunt when Dwayne Barry kidnaps Scully.
Moulder races to rescue Scully and has to contend with Krychek's betrayal and larger government forces at work. However, these episodes set up a moving payoff in "One Breath," where Scully suddenly reappears, comatose and slipping away. Moulder wrestles with grief while fighting for a way to save her life. The true tragedy is that Moulder can't accept Scully's death, but thanks to a miracle, does Scully come back to the land of the living, leaving the audience with many questions.
Following this, Season 2 continues with several monster-of-the-week episodes like "Irresistible" and "Die Hand Die Verletz." While "Irresistible" sees Scully hunt a non-paranormal serial killer, "Die Hand Die Verletz" confronts Moulder and Scully with a demonic cult of teachers. This episode leans into horror tropes with creative imagery. Morgan and Wong's departure leaves room for new talent like Darren Morgan, who writes humor-laden episodes such as "Blood" and "Humbug."
Outside standalone episodes, Season 2's myth arc, such as "Colony" and "Endgame," balance thrilling action and character drama, yet intertwining Moulder's personal history with the alien conspiracy becomes a point of criticism. Despite some shortcomings, the Emmy-nominated Season 2 poised The X-Files for greater success with Season 3.