There has been much suspicion that Skinner is against Mulder and Scully's work. In the first season, he is seen taking orders from the Cigarette-Smoking Man, which at first makes us think that he's on the dark side (sense the Star Wars theme?). Actually, as it is revealed to us later on, Skinner doesn't wish to be working for him, and warns Mulder against asking CSM for help. In one episode, Skinner finds the Cigarette-Smoking Man in Mulder's office..."You think I'm the Devil, don't you?" says CSM, seeing Skinner's expression, which shows his true feelings for the man. CSM has been known to do things to Skinner like smoke in his office when there's a no smoking sign, but the worst thing he's ever done, and this is my opinion, is to drop one of his cigarettes in Skinner's coffee cup. (You should have seen the look on Skinner's face, pure hatred) In the end of one episode In Redux I, the second episode of season 5, Scully suspects that Skinner has been against them from the beginning, working for a secret company called Roush, but it turns out that Section Chief Blevins was the traitor. (Afterwards he was shot in a way that made it look like suicide.)Skinner actually keeps Mulder from quitting the FBI in one episode by telling him of his experience in Vietnam, and how he didn't want Mulder to give up now like he did, because then they would win. (There's that they again!) In the episode Piper Maru, Skinner gets shot in the small intestine (ouch!) by the man that shot Scully's sister, Luis Cardinal. He helps Scully find the shooter, who then gets killed in his jail cell, also meant to look like suicide, but we all know it wasn't. In End Game(I think), Skinner violently confronts X, Mulder's secretive source, and gets the information that he wouldn't tell Scully. In many inderect ways he has saved the agents' lives.
Skinner, like Mulder and Scully, suspects a greater truth that the government is hiding, and luckily he has Mulder and Scully to find it.