I'm not sure if you're asking about collapsing the trajectories to a single value per ship, or just displaying a binned version of the scatter? If it's the latter, binscatter (or histogram2) might solve this problem.
x=randn(1000,1);
y=x+randn(1000,1)/3;
nexttile;scatter(x,y,'.');title('scatter')
nexttile;binscatter(x,y);title('binscatter')
nexttile;histogram2(x,y,'DisplayStyle','tile');title('histogram2')
c=colorbar;
c.Label.String='Count';
