Mulder's computer changed! In "Little Green Men", he has a Mac. When Scully checks the email on Mulder's computer in this ep, it's clearly a Windows™ machine. Specifically, it's either Windows 3.0, 3.1, or 3.11.
Isn't he allowed to change computers?
A nit I can't believe Phil overlooked: when mulder finds the sub, there is huge lightsource behind it - and its not the beam of mulders flashlight! (The flashlight can be seen as seperate beam). And it can't be some light from the sub itself, since its without power. Almost like a stagelight from its effect.
Phil wondered in the Guide why the bounty hunter hung around the sub for 5 days, and how come his UFO was still flyable after the crash. Maybe it was damaged, and the bounty hunter was working on getting the sub operable again, so he could drive it to his craft and repair it with parts from the sub itself?
Why does Scully say at the end that neither the sub nor the UFO has been found? How can a whole sub - a big mass of metal - vanish? Shouldn't it be easy to find, esp. if a whole fleet is in the area? (They found mulder - a lone human in a vast ice area!)
Phil also remarked that the fins made no break in the ice coming up. Maybe the ice reformed in the 5 days since?
I still think the ice around the sub looks terribly fake.
when mulder finds the sub, there is huge lightsource behind it [...] And it can't be some light from the sub itself, since its without power.
A good point but all US Navy vessils have seperate, battery-powered lights called "battle lanterns" that are seperate from the main battery.
In the Guide Phil was fortunate to get some info from a submariner who attended his church, and all the points made about the USS Allegaince where correct, however there were more he either missed or edited out. For one thing, I don't know where TPTB got their model from but it definitely isn't a US vessil. Also, Phil inquires why there wasn't areas in the ice where the fair-water planes came through (those extentions that look like wings which rotated vertically to submerge at the end, and constanze provides a good explanation) but in reality those planes would stay vertical the whole time it is above ice and there are no lights on them or the sail like we see here.
The captain says they are on a cartography mission to an admiral on the phone, when supposedly he is ordered to engage the ship. This is not a job a military force would be doing, especially an attack submarine. They could possibly be recording the glacial movements/formations but this is futile since they are always changing.
Why, after what he's learned from the death of SA Weiss and what 'Samantha' has told him about alien blood being toxic, would Mulder shoot at the bounty hunter, especially when he wasn't even aiming for the back of his head? That wasn't all that bright and added unnecessary drama to an ep. that already had quite a bit.