I honestly didnt understand any of it apart from that Sarah is still alive. 
Who the hell is Reed?? I get that Kobin was th guy that produced the fake Sarah, but then I'm lost after that, like COMPLETELY lost!!! 
Just if anyone could explain what the hell went down, and what the explanation Reed gave at the end meant, I'd be most grateful!! 
Cheers!!

Okay, so, mega spoilers. 
 

" Okay, so, mega spoilers. 
 

SPOILER WARNING: Click here to reveal hidden content.

The game starts and Sam has left 3rd echelon after his daughter died and he was forced to murder Lambert during Double Agent. Grimsdottir leads Sam to Kobin, and Kobin reveals that 3rd Echelon paid him to supposedly kill Sam's daughter. The 'meeting' with Kobin was actually a trap to capture Sam by 3rd Echelon. We find out from Grim in america that the new head of 3rd Echelon, Tom Reed, is up to no good, and she is actually a mole inside 3rd Echelon for the president. They want you to stop Tom reed since you're technically not a part of the US government and you can work your way from the outside. 
 
Grimsdottir reveals that you daughter is alive, and you get a message from her part way through the game, but the principle twist isn't until later.  

The rest of the game kind of follows your attempt to stop Reed, until you go to Grimms office at third echelon. Here she reveals that it was your old handler, Lambert, who plotted to fake Sarah's death. he discovered that there was a mole inside 3rd Echelon, and that somebody was going to try and kill Sarah Fisher. He ordered Kobin to kill somebody that looked like Sarah to trick Sam. He did this because he wanted to keep Sarah safe, by making her think Sam was dead, and to make sure Sam would remain at third Echelon, thinking it was a random hit and run rather than an assassination.
 
So Sam finally confronts Reed, and he reveals that there's an international organisation that he's working for called Meggido (you hear the name earlier in the game, but you only learn what it means here). They wanted to kill the president so that the Vice President, who was sympathetic to their cause would take over. Reed wanted to kill the President because she wanted to get rid of 3rd echelon. Sam also figures out that it was Reed who was the mole Lambert couldn't find in third echelon.

"

Don't mention it : )

Speaking of the story,  

Sam Fisher's old, so now he becomes the voice in the ear of some new generation of spies, and since he's in charge now he makes sure everything is on the up and up.  Boom, sequel.

" @End_Boss: Sam Fisher gets his hands on  a Time Machine. "

" @JustTheDoctor said:

" @End_Boss: Sam Fisher gets his hands on  a Time Machine. "

And what will he do with that? "

" Sam Fisher's old, so now he becomes the voice in the ear of some new generation of spies, and since he's in charge now he makes sure everything is on the up and up.  Boom, sequel. "

"I'm pretty sure that he just wants to go home and spend some quality time with his daughter.  HOWEVER... the very end with Coste being interviewed, the lights going out, and shit going down, it does seem like he could be back on -some- case. "