As we know in the Season 3 Finale, the Governor slaughtered his soldiers and ran off with Martinez and Shupert, but they didn't go back to Woodbury where could they be, and what will become of them?

This is my personal guess:

The Govenor, Shupert, and Martinez will stumble upon a National Guard armory, they will gather guns, food, gasoline, and cars. They come across another group, and a masked Martinez and Shupert lead a raid on them and kill and wound some of them. The Governor blames the deaths on the Prison group, and The Govenor enlists them with the promise of supplies and a safe haven (the Prison).