In 2014, IDW published The X-Files Conspiracy: Teenage Mutant Ninja Turtles by Ed Brisson and, Michael Walsh, and Miran Kimi. This issue was part of an IDW crossover that saw the X-Files world mix with the other properties under the publisher including The Crow, Ghostbusters, TMNT, and Transformers. The event follows the Lone Gunmen as they try to save humanity from an impending plague that will end most of the world. While Agents Mulder and Scully are investigating one lead, the Gunmen decide to investigate multiple urban legends which leads them to run into multiple characters, setting up for multiple crossovers.
In The X-Files Conspiracy: Teenage Mutant Ninja Turtles, the Lone Gunmen encounter the Teenage Mutant Ninja Turtles believing the Turtles are part of an urban legend, making them a primary target for their investigation. Deciding to travel to Northampton they encounter both the TMNT and vampires, a bit more than the Gunmen had expected to find.
The issue begins with two people exploring a forest and while roaming, they make a startling discovery. Later, the Lone Gunmen visit the same forest where they find that what had shocked the couple before is a human-like turtle. The Lone Gunmen think these are the sewer creatures they have been looking for and we learn that the Turtles are hiding from the Foot Clan, and are growing antsy from lying in wait. The Lone Gunmen arrive at Northampton and find that out animals and people have been drained of blood, an issue plaguing the town. They think that this has to do with the sewer creatures, so they investigate further. The Gunmen learn that everyone who has died had ordered food from Golden Pizza on the night of their deaths and, even weirder, is that all the victims had their shoes removed.
Meanwhile, two of the Turtles' friends go into the Golden Pizza, while The Lone Gunmen wait for the sewer creatures in the shadows. The Turtles keep a close eye on their friends, April O'Neil and Casey Jones, as they're worried about the Foot Clan showing up and attacking them. When a chair is thrown out of the window of the pizza place, both the Turtles and the Lone Gunmen run to Golden Pizza. They all discover that the Golden Pizza cooks have knocked out both April and Casey, and are in the process of removing their shoes. The Turtles attack only to be confronted by more Golden Pizza workers.
After calling Mulder, they find out the cooks are a group of vampires led by Ronnie Strickland who move from town to town, feasting on people's blood. At Mulder's advice, they throw chili flakes onto the floor, because vampires are known to stop what they are doing and pick things up off the floor. This leads to them running away before getting caught, but before the Turtles can pursue the vampires, the Lone Gunmen ask them for samples of their blood. They believe that the samples may help to create a cure to stop the incoming plague. The Turtles deny the request and head home, but Leonardo seeks the Gunmen out and reluctantly agrees, but not without threatening to hunt them if he finds out they are lying.
The Lone Gunmen in the original X-Files series provide a more comedic standpoint than Agents Mulder and Scully are accustomed to and in the case of this crossover, it works very well. While Mulder and Scully tend to be the main investigative duo, they also tend to be more stone-faced than their conspiracy friends, and the Lone Gunmen's humor matches perfectly with the urban legends they investigate.