Plot hole: Wilmore keeps busy (or straight shoots, really) the two agents outside Rauch's house. Meanwhile, Mulder leaves him to get to the secret facility. One wonders how, since they are in the middle of Alaska, he doesn't have a car, and there's no reason why he wouldn't help Wilmore killing the bad guys, so he can get his car, or the agents'.
Factual error: You decide to investigate the russian ship "Tarakan." The captain says "it's not far from here", and the characters take what looks like a leisurely stroll on the dock from their position. If you look at the in-game map, the two dots are on opposite sides of the bay.