With cries of "Sic Semper Tyrannis", nearly a quarter of the United Empire's worlds have seceded to form their own nation. They call themselves the Pilgrims. The Empire interpreted this secession as treason, and the overwhelming might of the loyalist fleet has fallen on the Pilgrims. Although the situation is militarily hopeless, you have a secret communique from the Sophon that could end the war. Get to the Pilgrim Council.
Otherwise empty sectors now give you the opportunity to talk to members of your crew. Your relationship with them changes over time as you progress through sectors.