X-Files leads Mulder and Scully encountered some strange and eerie phenomena over the years, but they almost investigated Abraham Lincoln's ghost. While the pair of FBI agents probably would've been surprised to meet him, it's likely Mulder would've just wanted to ask Honest Abe if he knows the truth that's out there. To be sure, the idea of Mulder and Scully connecting with the 16th president of the U.S. is a premise that seems ripe for comedy, but thankfully, that's an area The X-Files often excelled at.
In fact, some of the greatest X-Files episodes ever made were funny and/or silly, such as "Bad Blood," "Jose Chung's From Outer Space," and "Mulder and Scully Meet the Were-Monster." While it's possible that Lincoln's ghost appearing would've been played straight, it's highly doubtful, as there's no way Mulder and Scully would be able to resist unleashing some dry-witted zingers about how ridiculous it is that they're even entertaining the idea that this particular reported haunting is true.
Of course, as any X-Files fan knows, there were never any Abraham Lincoln sightings on the show, nor did any other dead commanders-in-chief make an appearance. It's sad that the idea got tossed aside, as it really could've been a great farce in the vein of something like "X-Cops."
X-Files Almost Included Abraham Lincoln's Ghost: Why It Didn't
The reason fans get to know that The X-Files almost featured Abraham Lincoln's ghost is a 1997 Cinefantasique interview (via Eat The Corn) with writer/producer duo Glen Morgan and James Wong. Morgan and Wong crafted some of the best X-Files episodes and later went on to guide fellow Chris Carter show Millennium for a while. Near the middle of season 4, Morgan and Wong set out to write a story in which Lincoln's ghost would be seen haunting the White House, leading Mulder and Scully to be sent in to investigate the reports. Morgan especially wanted to bring this idea to fruition, as he had considered writing a feature film featuring the spectral president, and had done lots of research on the man already by then.
Unfortunately, Lincoln's ghost not haunting The X-Files actually has ties to an entirely different script. Around the same time, Morgan and Wong were repeatedly forced to do rewrites on their script for "Musings of a Cigarette-Smoking Man," which delved into a possible backstory for the mysterious villain. The duo weren't pleased with either the amount of changes or their content, and Morgan decided not to offer his labor of Lincoln love to The X-Files any longer. He and Wong scrapped the idea, and wrote the Scully-centric "Never Again" to take its place in season 4.