Awesome stuff, eh? :D Okay, so...
The ABH crashed his UFO in the Beaufort Sea right at the start of episode "Colony", if you recall. It happened after the opening credits. There was a crew observing the UFO hovering and then it crashed into the sea. Later a news report talked about it prior to the first doctor getting killed. So his crashed craft was then recovered later by the submarine in episode "End Game". He didn't intentionally hide it below the ice. It just crashed there. In regards to your question from the previous episode "why do they always crash?"... think of it this way: We are only being shown the UFOs that crash, not the ones that land perfectly. :)
Like I said regarding "Colony", Samantha really didn't say Bill Mulder was in danger. When she said "my father" she was referring to her adoptive parents. I felt like addressing this again because you mentioned it again.
You missed two really well done morph VFX, looking away from the screen just at the moment the ABH does a morph, in this case Mulder -> ABH, and later submarine guy -> ABH.
Speaking of which, the submarine guy was the same guy from the teaser (prior to the opening credits). I'm not sure you recognized him. He was the guy who was hesitant to fire at the unknown craft prior to the submarine getting disabled. ABH took his shape at the end of "End Game".
Great call about Samantha being a clone! :D Now, the "special" Samantha that they show behind that door in the facility, and say she's the one they all came from... they mean that she was the first clone. Not his real sister, but the first clone of his sister.
A good question you ask is whether the ABH is really an "alien" or an alien-human-hybrid. I'd say that you should think about this in a simple manner: Would an alien-human-hybrid fly a UFO from outer space and try his best to return to it in order to fly away again? Logically speaking, at this point, everything points to him being an alien.
The ABH uses the "alien stiletto" to pierce the back of their necks. You seem to have realized this later in the episode. Samantha "thinks" that a gunshot to the back of the neck will work, but she's not certain if it'll work. It is for us to think about whether he was shot in the right place and survived nonetheless, or whether they missed the spot. Another question for us to think about is, maybe there's a reason the ABH uses that stiletto weapon instead of a gun. They obviously weren't able to kill him with a gun/sniper. Again, either they missed the spot, or a gun is not sufficient.
In terms of this two parter being a game changer, it definitely was for me and plenty of other fans. But you'll get people who feel similarly about the "Duane Barry" arc (including "One Breath"), whereas for others the season one finale was already enough to get them hooked, or a standalone episode like "Ice" for example, etc., but yes, this two-parter was huge when it came out.
Either way... great video. I'm glad you enjoyed it!