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In order to gain the Leadership skill, you simply need to complete "The Liberation of the Black Pearl" Story Quest by completing the boss battle. After you complete the boss battle, Jack Sparrow gives you Leadership.
The "2nd Quest" that you are referring to may have to do with the small chain of final tasks between gathering all the recruits, and the Boss Battle. As of now, there is no official information of the Second Story Chapter.
P.S. Just as a side note, when the time comes, if you need help with the Boss Battle, just ask.
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