I have recently bought and downloaded all the DLC's and I finished "Take it back!" with the option to let Fawkes (My Meta Human companion) activate the purifier for me since "Hey, he is immune to radiation, why not?".
Big mistake.
The Broken steel storyline didn't start.
I did see the "Two weeks later" cutscene, but I continued NOT from the clinic in the citadel, but in the Project Purity room with everything just how I left it.
Elder Lyons or anyone else won't give me any special dialogue options and I am basically screwed on the Main Quest.
I still have a very enjoyable amount of roaming and side quests to do but I would love to finish kicking the Enclave's asses.
Data file load order (according to FOMM):
Anchorage.esm
Fallout3.esm
ThePitt.esm
BrokenSteel.esm
Zeta.esm
CRAFT.esm (Community Resource to Allow Fanmade Tinkering, allows making custom schematics.)
CALIBR.esm (Community Ammunition LIBRary, I'm guessing this adds more ammo options.)
FO3 Wanderers Edition - Main File.esm
EVE.esm (Energy Weapons Enchanced)
FO3 Wanderers Edition DLC support esp's
GalaxyNewsRadio100[M].esp (Extends GNR's playlist by 100 songs.)
To anyone that contributes, thanks.