 Scully can be seen handling the two coins fused together from  episode #6.4, "Dreamland" and the dog tag from episode #3.22  "Quagmire". She also gives Doggett the Apollo 11 medallion from Max.  Agent Leyla Harrison mentions that their suspect may be "a liver  eating mutant", saying that Mulder and Scully have killed one. This  is a reference to episodes #1.2, "Squeeze" and #1.20, "Tooms".