You can access story quests through the top right window, under Quest Finder. You can check the cool down under Quest Log(Also found under the top right).

North - Boss South - First part of quest

1-3 minibosses drop gems, you have to take them and throw at the altar marked as “X”, 4th miniboss drops gem that has to be cleansed
After successfully cleansing gem, you have to take the gem with you and throw it at altar in boss area marked as “B”