- This troper doesn't fully understand why the terrorists put the bomb in the neighboring building and call it into the one the bomb squad were investigating. Why give it such a long time to detonate? What was their plan exactly? If they wanted to frame Mulder and Scully for not dismantling it (or whatever), how would they know Mulder and Scully would be in that building in the first place?
- As far as this troper understood, the primary goal of the bombing was to cover up the bodies of the virus victims. Mulder's involvement wasn't intended but Michaud was there for just such an occurence.
- Why did Scully, of all times and places, decide to prank Mulder while they're escaping a giant spaceship with angry aliens hatching everywhere? You'd think she'd be smart enough to wait until they weren't in mortal danger.
- I'm pretty sure she actually did stop breathing. Mulder definitely would've noticed otherwise, as he was in close proximity to her and Scully was in no state to pull off a convincing performance. Her playing it off as a prank was simply a way to defuse some of the tension.
- If the Syndicate was intending on kidnapping/killing/somethinging Agent Scully to manipulate Mulder, did they do the whole toxic bee thing on their own or was that just a happy coincidence while they waited patiently listening to the 911 calls to go pick her up before the real paramedics did?
- Then there's the big one: if Mulder's snow cat ran out of gas, how did he and Scully get home? And for that matter, with only one pair of winter clothes between them, how did they survive until they got there?
- There's no Word of God explanation (even in canon), but it's possible the Sno-Cat CSM was driving still had gas, or maybe a spare gas can.
Headscratchers / The X-Files: Fight the Future