Sea Dogs 2abandons the idea of nationalism, where players declared loyalty to one of several countries, and instead focuses on the development of the captain and his or her crew. Nevertheless, countries do play a factor in the title, as players may find themselves coming under fire from one of several countries, including France, England, Portugal, Spain, and the Netherlands. There is only one storyline for players (regardless of a male or female captain), but Akella promises it to be long and detailed. In addition to the main plot of the game, Sea Dogs 2will have a random quest generator for players to gain experience and gold between taking on plot specific missions.

New to the game is the concept of island ownership. One of the great challenges of the title is to rule over all ten islands. This is no easy task considering that the developers have now included armed rebellions and naval blockades. While players might have no trouble squashing an impudent uprising, an island won't be much good if basic items like bread are being embargoed. Players will have to manage both land and aquatic hostilities to succeed in Sea Dogs 2and Bethesda is letting players take as much control over their ship as they desire, whether they want to hoist each sail hand over fist, or simply order a destination, then sit back and watch the waves ripple by.​