Theta Protocol

Last thing he remembers, sensor technician Josiah Tracy of the Terran Navy FTL ship Capricorn was living his day-to-day life onboard the ship.

Waking up, he finds that he has become a cyber citizen, an uploaded consciousness that can live effectively forever in control of the Capricorn. Which happens to be heavily damaged, with no other survivors. And over 40 years have passed, which does not bode well for the state of the rest of the fleet. After all, with the Capricorn being the only FTL ship in the fleet, they should not have been left effectively derelict unless something has happened to the rest of them.

A space themed story, with a primary focus of rebuilding his ship and the fleet, exploring what happened to them and humanity as a whole along with alien exploration and interaction. Plus a subtheme of romance, of course. Since what is immortality, if you have no one to enjoy it with.