During X-Files season 2, Scully gets abducted and experimented on, taking her out of the picture for awhile, and here's why that story was written. Some have argued that Scully, played by the always captivating Gillian Anderson, spends a bit too much time as a damsel in distress in the early years of The X-Files, and the criticism is a valid one. To be fair, Scully did eventually evolve past that phase, for the most part. In season 1 though, Scully usually wasn't apart from Mulder for long.
The quickly solidified bond between Mulder and Scully - and also fans' bond with the characters - was tested in season 2, with Scully being taken, barely appearing in the following episode, missing the next one entirely, and spending the one after that confined to a hospital bed. In the meantime, Mulder spent his days and nights first searching for Scully, then working cases by himself, then trying to get to the bottom of what happened after Scully's mysterious return.
Some may wonder why creator Chris Carter and The X-Files writing staff made the choice to sideline Scully for an extended period so early in the series' run. Well, it turns out that doing so wasn't their original idea, but real life events stepped in to change things.
Why The X-Files Season 2 Had To Rewrite Scully's Character Plan
Gillian Anderson's first marriage was actually to an X-Files crew member, assistant art director Clyde Klotz, who she met while working on the show. That's relevant to this story because near the end of filming season 1, Anderson became pregnant with their daughter Piper Maru, who later got an episode named after her and actually worked behind the scenes in the art department on the recent revival seasons. While tricks were used to try and hide Anderson becoming visibly pregnant, it became clear that she would eventually need at least a brief maternity leave from The X-Files.
That led to the creation of the "Duane Barry/Ascension" two-parter early in season 2, which sees Scully get abducted by either aliens or the government or both. She's then gone for awhile, much to Mulder's dismay, only to reappear mysteriously and spend some time recovering. This limited role for a number of episodes allowed Anderson to get her leave in while still allowing Mulder to anchor new X-Files episodes. What's cool about the whole situation is that a storyline born out of necessity ended up becoming one of the key events in the entire mythology arc, proving once again that necessity is the mother of invention.