Meiam said:
Why was it bad that the enclave were the one who turn on the water purifier? That wasn't even addressed.
There is a reason, just sloppy in it's delivery.
In Fallout 2, the Enclave wanted to make a modified version of FEV that would "purify" the wasteland. Anything that had been exposed to FEV would be killed. However, since more than 80% of the population of the US has been exposed to FEV to some degree, it would wipe out nearly all humanoid life (ghoul, super mutant, or wastelander) and all mutant wildlife. In Fallout 3, they want to continue this weird scheme. Instead of being an air-borne pathogen... they want to contaminate "Project Purity" with a similar death juice.
Not only is this painfully inefficient, but they don't communicate this fact until very late in the game (after Liam Neeson kills himself). As a result, you can assume Colonel Autumn did a cartoonish monologue detailing the evil plan to Liam Neeson off-screen, or Liam Neeson can read minds and/or see the future. It is entirely left up to the player to fill in this gap in the story.