To start out you go to the tower and see who gives you a quest. If there aren't any then jump into the taken king story. From there get gear get levels rise repeat fun.
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How do I know where I'm at in the story? I have no idea what mission or quest I'm supposed to do next..
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Well the quests are tied together based on story and not level or expansion as much anymore so just grab whatever you see and just start going. I'm not really sure how they handled cases like yours but I would say just pick a quest and roll with it from there.