I can't remember if I got it the first time I went to the helm but it's not in my inventory and I have no quest for it. I've only got 8 quests in my folder so it's not full. I've looked in the mail for lost items on the helm and it's not there. Is there some sort of pre-req quest I'm missing? I just came back after not playing since red war.
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After completing the Salvage and Salvation Quest, you are lead to to the Last City where Spider gives you the Ahoy and Aweigh Quest. This quest ends with visiting the Starchart and begins the Sales Of The Shipstealer quest. After listening to a holoprojection of Mithrax, the Atlas becomes available.