The “later” he is referring to is most likely the first season X-Files finale, one in which Deep Throat risked his life to save Mulder and was subsequently killed. Therefore, “Fallen Angel” seals this character’s fate by more definitively making him a good guy, one who is inevitably on a collision course with the evil government conspirators that eventually kill him. Sadly, the murder of Deep Throat sets up a kind of running theme where many allies who try to help Mulder out (including everyone from Max Fenig to Deep Throat’s replacement, X) are eventually killed.