I have been playing Fallout 3 on PC with mods for a little while, and then had some crashing issues so had to reorganize some mods. But when I got it running again, almost all the story line after finishing the quest Project Impurity no longer shows up. There are no longer crates of Aqua Pura in the Citadel and the Jefferson Memorial is reverted back to Enclave/mutant control. I still have Fawkes as a follower though. I used the command "resetquest 00014e93" then "Completequest 00014e93" (on a separate save in case it made things worse), and it showed "Quest completed Project Impurity" which also shows under my competed quests in pipboy, but the game play still doesn't show the purifier up and running (the route I chose when completing the main quest line). I have no idea how that data got lost or how to retrieve it.