Tad O'Malley arrives to pick Mulder up in his helicopter, and later Scully visits and they discuss the conspiracy in episode 10x01 "My Struggle". Scully talks to Mulder at his home in episode 10x05 "Babylon". The house is attacked by a small team of private military contractors in episode 11x02 "This". Appears in 1 more episode.
Mulder and Scully arrive at Sveta's house in Tad O'Malley's limo and question her about her abductions in episode 10x01 "My Struggle".
A young Skinner is tasked with transporting a mysterious crate during the Vietnam war in episode 11x06 "Kitten".