There doesn't see to be a clear reason of why she was alone, but the conversation that Ikuta and Torway had seems to imply that something shady might have been going on. First, we know that she is the third Imperial Princess, meaning she is a candidate for the succession of the throne. This means this could have been a plan to possibly get rid of her. Second, If I remember correctly she boarded the ship alone because she was looking for promising new officer candidates who were not part of the already corrupt government. Since she wants to try and save the country. Never read the LN or anything, but these are some of the reasons that seem to be implied. Sorry if this wasn't much help.