Talk to Danse in the Cambridge Police Station. After the conversation, you need to talk to Rhys or Haylen to get your assignments. Rhys will give you the sub-quest "Cleansing the Commonwealth" while Haylen will give you the sub-quest "Quartermastery". These sub-quests are repeatable, including sending you to the locations you previously cleared, allowing you to collect the common loot you have acquired before. This sub-quests also give a considerable amount of EXP and caps, making it easier for you to grind.
Completing at least one objective for each will complete the quest and unlock the next brotherhood quest, The Lost Patrol.