Super Soldiers

I have a theory on the Super Soldiers. I like to think that there are two kinds of Super Soldiers...

1) Man-made Super Soldiers that the Syndicate was working on developing back during (maybe before) the Vietnam war. We see references to humans with extraordinary powers in the episodes "Sleepless" and "Eve", and then we are introduced to the Super Soldiers that fought in the first Gulf War. I believe these Super Soldiers were created by the Syndicate/US military in order to combat the aliens during invasion. By the time season 9 rolls around, these man-made Super Soldiers are a success (with few weaknesses such as magnetite), and that is why the Syndicate has been adding a substance to drinking water in order to begin altering unborn children in order to make them naturally-born man-made Super Soldiers, which is what baby William was.

2) Alien-made Super Soldiers, somewhere along the line the aliens who are planning on colonizing the planet found out the human beings were creating a Super Soldier to fight them, in order to prevent re-colonization of the planet by the aliens. The aliens began abducting human beings and transforming them into alien-made Super Soldiers in order to have aliens capable of nearly the exact same strength as the man-made Super Soldiers. People who were abducted in season 7's "Requiem" were taken and genetically altered during their abduction to be returned to Earth and reborn as alien-made Super Soldiers: Billy Miles, Fox Mulder, etc. Theresa Hoese would have been one of these types of Super Soldiers, only Jeremiah Smith (one of the good aliens who seems to want to prevent colonization) was able to "turn off" whatever the aliens did to her during her abduction so that she would not turn into an alien-made Super Soldier. The way I understand it, as this information was provided to us in season 8/9, is that if Jeremiah Smith did NOT help these abductees who were taken at the same time as Mulder (including Mulder himself) that they would become these alien-made Super Soldiers. Theresa Hoese was lucky, but Billy Miles and Fox Mulder were not.

I think that somewhere inside Mulder this genetic mutation is lying dormant and waiting to be released to take Mulder to a final transformation into an alien-made Super Soldier. Whatever Scully did to "save" Mulder from this transformation in season 8 is just a temporary fix, and that he is still susceptible to becoming an alien-made Super Soldier simply because Jeremiah Smith is the only thing that can prevent this from happening, and since Mulder was not saved by Jeremiah Smith right when he was found dead, that it is too late for Mulder.

I don't think that the aliens can touch baby William. He was a natural-born man-made Super Soldier, and Spender may have injected him with some form of magnetite to make him normal, but how I think Mulder's alien-made Super Soldier junk is dormant inside of him, I also think that the man-made Super Soldier junk is dormant inside of baby William - and that eventually the story could turn into father against son in the fight for human survival on the planet. And of course, baby William would win, thus saving the planet and the human race from the aliens :)

This is all just my take on the Super Soldier aspect of the series, and I've thought this for so long that I'm sure that if it turns out to be different that I'll be disappointed (another reason why I don't want XF3 to happen). It's all theory based off of information provided to us about Super Soldiers in the last two seasons of the series.

Agree or disagree, I just thought I'd put this out there for you guys to contemplate :)

Addendum to the post above...

The aliens came to take Jeremiah Smith away at the end of "This Is Not Happening" (you know it, when Scully falls to her knees and howls). The aliens are taking Jeremiah Smith away at this time because they know that he is the only one capable of making sure that abductees returned to become alien-made Super Soldiers do NOT turn into Super Soldiers to combat the man-made Super Soliders when colonization begins.

The aliens were going around the country/world around the time of "Requiem" to abduct those people/previous abductees who have the same genetic anomaly as Gibson Praise (the same junk DNA that Mulder had activated in "Biogenesis") - so not ALL alien abductees are capable of having their genetics manipulated so that they become alien-made Super Soldiers. This explains why Scully wasn't taken in "Requiem" and why Mulder was. Scully's got normal DNA, nothing that the aliens require in order to transform her to a Super Soldier, as they did with Mulder.

Does this help answer any questions that you may have been thinking while reading the post above?

You know, this totally makes sense and I may just save this thread for my story since you have such a clear view on it. Or I could just pester you in person. This is a very cool idea, too bad we couldn't have seen it all the way on the show.

Thanks for the explanation, it makes a little more sense now that I 'know' that there are two sorts of Super Soldiers (should have red this before I posted on the s8 rewatch ). It's a shame that CC didn't write is as clear as you discribe it here, I think your idea would make a very good X3 (father against son), it could tie up many of the loose ends, though I understand that you would not be a happy camper when it would be portrayed as a whole different story!

As Little Albatross pointed out, your theory about Mulder's genetic mutation would be a good plotbunny...
And it makes a lot of sense.