On this playthrough I decided to insert the FEV received from President Eden into the Purifier.

So what is the result?

I still get admonished for not taking the "selfless path of my father" or some such nonsense. Yes, I had Fawkes activate the Purifier. He is immune to radiation.

Doing it myself would literally be committing suicide. (and I assume end the game?)

BUT, after I wake up in two weeks, Fawkes is right there next to me, and continues to follow me into the wasteland. How does he survive that?

The slideshow after the purifier is activated shows Supermutants, Raiders, and Ghouls among the victims of the FEV.

So the only enemy left out there is the Enclave?

Broken Steel essentially breaks the FEV ending, since the creators originally intended for the game to end at the Purifier. Thus, you have people just get tummy aches instead of the widespread cleansing that the ending actually implies.

As for the narration, yeah that never made any sense either. And its laughably moronic. It seems to think that letting your super-mutant buddy who's completely immune to radiation start the purifier and save yourself the trouble of having to kill yourself, is somehow wrong.

Fallout 3 isn't exactly know for having a solid story, or a coherent narrative.