X-Files crossovers. The whole concept has become an indulgence for most fanfic writers. An attempt to graft the dark world of shadowy conspiracies and secret cabals to the world of brightly colored spandex and giant robots which never cause too much damage to the city they protect.
But there's no one who has ever done a better job than Stephanie Moffett. These were the first two PR fanfics that I ever read, back in 1996. And I think they still hold up. Steph has a gift for being able to bring the disparate elements of these programs together, into a unified whole.
Missing begins with what seems like a straightforward abduction case. Except that the kidnapped teens happen to live in a city with no crime or murder rate. A city under the protection of superheroes, facing a very public invasion from outer space. To tell you more would ruin a lot of the fun of the story, so I won't get into detail.
Disappearing Act picks up one year later, after Billy vanishes following some very erratic behavior. Rocky enlists the aid of Mulder and Scully, two of the only people in the world who could investigate this case (given how much it pertains to the Rangers), and ends up dragging the agents into a surprisingly X-Filesian assignment. While this fic is slightly more over the top than its predecessor, it gets bonus points for giving us the classic "allude to everything, explain nothing" ending X-Files is famous for.
These stories are the reason doing an X-F crossover tends to rank so high on the personal goals list of most fanfic writers. Much as how Out of Time inspired a lot of Wicca symbolism in fanfics dealing with the magic of Power Rangers. Once you see something done as well as it's going to be, you tend to want to emulate it. Found at Paladar's World of Fanfic and The Fanfic Shoppe.