okay so quick questions that i would like to be answered.

1) who is that random sniper guy who comes out of nowhere and talks to you after you fell off the helicopter?

2)where did the sniper guy and MAG go when you parted ways?

3) where was he when MAG ran in and got killed?

4) did they ever explain what the blue glowing pod thing is that you get at the archives and why they want it?

5) what were those random vulture things and what were there purpose?

6) what was Super Joe's main goal?

I need these questions answered because right now, this game makes no sense to me and i am starting to think that after they got done writing the concept that Emily was apart of the arm they just gave the keyboard to over caffeinated 13 year olds to write the rest

The story wasn't really written as well as I had hoped.  I have similar questions as well, but let me try to answer:

1. Random sniper guy is SILVER.
2. SILVER probably went to get a sandwich.
3. SILVER was enjoying his sandwich and decided to get some root beer and chips.
4. Blue glowing pod was the Carrion thingie.  That's used to power the Vulture army and Super Joe's suit.
5. The Vulture bots are supposed to be a part of the new Project Vulture, which is supposed to be a top secret weapons project along the lines of Project Albatross from the NES Bionic Commando or Bionic Commando Rearmed.  It's supposedly so powerful that whoever has this could possibly rule the world.  At least that's the impression I got with the whole "don't let the enemy get their hands on it" spiel I got from the Secretary and Super Joe.
6. I'm still trying to answer this myself.  I think Super Joe wanted to take control of Project Vulture so he could threaten the FSA government to make Bionics legal again.  Super Joe was always a huge supporter of Bionics (he called himself the "father of bionics") but didn't have the power to make the government reverse the order to make Bionics illegal.  If he had Project Vulture, he could threaten to destroy the FSA if they did not allow Bionics to be legal again, or take over the FSA and rule for himself.

As for SILVER, I'm lost as to who it is.  I'm thinking that with that one big eye, I thought he might be the Leader except a fragment of his face survived or something.  He's apparently linked to Bionic Commando's past, whether in Rearmed or in another storyline.  Truth is, no one knows.

i just hate that they wrote it that way. this wasn't in my original post but it is dumb to make the big reveal that super joe was the villain in the mask because they only show that guy once in the whole game. and later after the sniper guy shoots the gun, Nathan just accepts the crap that is given to him from super joe.

Also I had no idea about what all the stuff with Emily was about

Super Joe is Silver. Super Joe wants to rule the world. Do you need any other explanation for a villain? :P
Emily needed to sacrifice her life as a catalyst for Spencer's Bionic arm to function. In lamen's terms, her 'soul' is in the bionic arm. She says that Spencer is the one who was lost because he took the disappearance of his wife very harshly and was tormented by it, even tho she was technically with him the whole time.
Sniper dude seems to be one of those characters that are only around to help out randomly in a couple of plot points. He stops the two good guys from killing eachother, and he 'patches up' Spencer after his fall from the helicopter. Super Joe calls him a relic, since he is probably aware of his presence but does not consider him a threat. He wasn't around when Mag was killed to elevate the intensity and emotion of the scene ;)

ah, that makes a bit more sense

.... no it doesn't! characters shouldn't be aware of emotional intensity, MAG and sniper guy weren't walking to the vault and stopped and said "oh wait i should leave to make this more intense, you go ahead mag" 

Yea the sniper bit still doesn't make a whole load of sense I was talking more about the Emily part

Super Joe's whole point was world domination through Bionics.  If he could enslave the entire population of humans, then he would have limitless Bionics capabilities.

HAHA, it seems I was wrong about the Silver thing.  Sorry guys.  I didn't get who Silver was until I looked at the BC website and went through the character profiles WITH pics.

I read more about the sniper guy online and in the credits, names him as Thomas Clarke.  If you know, he is one of the characters from the arcade game MERCs, where Joseph "Super Joe" Gibson also starred in.

How the hell was I supposed to know that!?
They don't show his face or say his name, and I'm supposed to logically say OH LOOK, IT'S THAT GUY FROM AN NES GAME THIS HAS ALMOST NOTHING TO DO WITH.

Haha i think the story is completely forgettable. Once Groeder died i stopped paying much attention to the voiceovers (that dude was awesome! vy aa you hidink spenceeeeh ). It's clear to me they simply wanted a way to tie past games into this new one, through characters or dialogue references. It's a complete mess, just completely botched. I couldn't give less of a crap. Nathan falls from a helicopter, gets off the ground, first thing he says is "Fuck! Shit!". That's the kind of script this is. Do yourselves a favor and focus on swinging around killing dudes. The less you pay attention the better.

Nice twist with the wife in the arm though. That creeped me out a good bit. Also, awesome jumping around on the bird bots. Woo! Explosions!