I JUST COMPLETED FALLOUT 3 - ENDING - OBVIOUS SPOILERS
Once you get that Vial from President Eden, then go to the Citadel, give the Vial to the Elder, then follow his huge robot thing to the Control Room for Project Purity.
I advise you save in a seperate file, because as soon as you go in the control room with Sentinel Lyons, you cannot exit the room. Go up, kill Colonel Autumn, input 2-1-6 as a password, activate Project Purity.
Then you die, (you get an achievement for completing the quest on the 360 version) and it's back to the title screen.
It's game over either way, it doesn't matter if you or Lyons activates the Project.
HOWEVER, if you keep the Vial and contaminate the project, well I don't know what will happen and if it ends the game or not, but I will check this out.
SPOILERS END