I was mulling over an interesting connection between and the symbolism that exists in this episode and Closure (season 7, episode 11).

In Closure, Mulder is watching the first Planet of the Apes in his hotel room. (/At the end of the episode he finds closure in the search for his sister who was taken by the walk ins, and has become a child of starlight. The Planet of the Apes movie mirrors the over all series plot in that the ape government conspires to hide the existence of an intelligent civilization that predated the rise of the Apes, whose small extant population evolved into apes (founders). Taylor is determined to find the truth regardless of the consequences and ultimately does in the ending scene to his dismay. Mulder, however, ultimately learns the truth, but he is relieved in finding it -- the ultimate fate of his sister.)

In the Founder's Mutation, we see Escape from Planet of the Apes playing in the hospital, in the scene where Agnes is pleading for help escaping. The movie involves Zira and Cornelius traveling back in time following the destruction of their future time line. Like Mulder and Scully, the nature of Zira and Cornelius' work and what they represent puts them in danger. They must eventually flee for their safety and the safety of their son. (/Their son is then given up for 'adoption' to Ricardo Montalban and raised in a traveling zoo. This mirrors the over all series plot regarding William.)

Later in the episode we see Mulder viewing 2001: A Space Odyssey in his daydreams with his son William. He specifically references the obelisk and jokes a little about the varied interpretations. The obelisk, as explained more thoroughly in the book is an ancient alien technology that allows those in its presence to abruptly/spontaneously transcend their current state. Early apes move from simple sentience to sapience and eventually at the end of the film/book, David Bowman to transcend into a being of energy or a 'star child'.

The use of found alien technology (the obelisk) mirrors the plot of the season 10 premiere, where humans have discovered the downed craft and are using the scavenged technology for their own ends. The genetic material that was found is similarly being used for experiments to use them to develop a founder's mutation that will create a transcendent human (human/alien hybrid). The 'star child' mirrors the ending sequence of (/Closure with his sisters transcendence into a being of energy/light waiting to be born again.)