User blog comment:JoshofBlades/Why the Empire Should Prevail Over the Stormcloaks! (part 2)/@comment-97.145.166.237-20120225215129/@comment-68.33.146.51-20130725165318

The septim bloodline is not a memory, there are infact still living septims to this day, that are largely unknown. Heres some proof from the Wiki, "Andorak Septim was a male Imperial born during the Third Era, and son of Uriel Septim IV[1] . Upon his father's,Uriel Septim IV, death he was disinherited by a majority vote of the Elder Council [1] . Instead, the Elder Council chose Cephorus Septim II, his cousin, to be proclaimed Emperor[1], which he did in 3E 248. [1]

For the first nine years of Cephorus II's rule, mercenaries and those loyal to Andorak battled the Imperial Legion and City Militias[1]. To end the war, the Elder Council granted Andorak the High Rock kingdom of Shornhelm, where his descendants still rule today. "

My theory is, after the assassination of the Emporer by the dark brotherhood, the Elder Council contacts the Septim descendants and rises one to the throne, giving the Empire back to the Septims to restore is former glory.