Speaking to Cinelinx in an interview, Brett Douville, who was the lead developer on Star Wars Republic Commando, divulged details on the possible sequel being pitched at the time.
There were two competing stories that were being pitched, one being developed by Tim Longo and one by lead level designer Kevin Schmitt. In one, you would have played the side story of Revenge of the Sith and carried out Order 66, hunting down Jedi as a team. In the other, Sev would have been the first man in the Rebellion army — the tagline was something like, “Every Rebellion begins with a single soldier.”
Tim’s plan would have had Sev start the Rebellion army, training a new generation of soldiers to fight the Empire: In my own imagining, I like to believe he’d go after his pod-brothers and counter-program them so they could fight the Empire together. I don’t recall what Kevin Schmitt’s would have entailed, but I like to imagine there would be a mission where you’d rescue him.
Not many people who worked on the original game stayed on to LucasArts, and he doesn’t even know if the ideas were ever formally pitched to the studio. Sadly, with the purchase of LucasArts by Disney and its rebooting of all previous Star Wars canon, it doesn’t seem like we will ever get a true sequel and find out Sev’s ultimate fate.