I have beaten both the main game, the dark below, and the house of wolves story missions, but when I go to the progress tab, they are showing up as incomplete. Short of playing them again, is there anything I can do to fix this?
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Welcome back to Destiny! If you haven't been on since TTK launched, a few things changed with the release of version 2.0 last September. One of them was the introduction of the quest system. Because the quest system did not exist in year 1, nobody had completed the quest version of the year 1 content introduced with version 2.0. You can complete the quests by redoing the content if you choose, gaining rewards like XP on the way. You can also abandon those quests if you don't want to redo the content, with no impact on your progression in other quest lines or ability to access the missions later.