Remember telling elder lyons about the super mutants coming form vault 87? well if you tell him and you have already helped with the water quests and killed all the enclave Elder Lyons will give you a quest to destroy vault 87 and to find out more information about the super mutants on terminals and bring the data to him.
For your quest depending if you killed Sara Lyons or not he will give you a good amount of brotherhood soldiers and Sara Lyons to go with you to vault 87. If you killed Sara Lyons he will send "Paladin Rick" with you including the standard brotherhood soldiers.
When you reach and get into vault 87 the same way you did to get into it to get the GECK there will be more super mutants this time ALOT MORE and there will be terminals that have the info to bring back to Elder Lyons. The terminals wont have been there when you do the story missions but pretend they where there all that time
HERE ARE SOME IDEAS THAT THE QUEST CAN END:
1.You have to reach the main power generator in the Vault with a science skill of 78? you can rig the main power Generator to have a serious malfunction and blow up in 7 minutes? you have 7 minutes? to escape the vault from the way you came in. REMEMBER the main vault door is blocked by rads so you cant go out the front way.
2.This idea will involve the super mutant blood samples "QUEST" Paladin Tristan gives you to kill super mutants and to take the blood samples off them.
The brotherhood of steel devolpes a new weapon from the help of the mutant blood samples you gathered You enter the vault 87 and kill ALL the super mutants with it. This idea i think is not as good as the first one sorry
Thats it for now please comment. The ? marks mean you can input your ideas for it and ill see if i like it.