I don't see the entire thing being a rehash of deckers.die. There may be a mission or two, but if the description is to be believed, the whole point of this game is that The Boss is trapped in a simulation of Steelport that seems just like the original. As a result, I feel like as the game progresses, he slowly realizes that it's a simulation and eventually starts breaking the game with all of the super powers.
Personally, if I were to write this story, I'd have it start out with the Bank Heist mission again. This time, however, elements are wrong, such as Pierce crossplaying as Aisha, zombie Shaundi (if the story continues off of that ending), mascots instead of Morningstar, etc. Once you finish the mission, the point of view changes to reveal that the whole mission was the simulation, with The Boss already having been captured by the aliens. Then the rest of the missions are mostly new, with elements from previous ones, such as the sky-diving segments. Also throw in some old activities such as Fuzz and Septic Avenger.
Eventually, The Boss realizes it's a simulation when he starts seeing all of his old friends such as Carlos and Gat alive and well, so he rallies the troops, masters the super powers, fights the aliens and Paul the Saints Flow Can as they hop into the game to stop him, and eventually the alien overlord hops into the game himself for the final battle. Post boss, you decide to stay in the Dominatrix for the hell of it.
Of course, I expect Volition to do a far better job, but that's just the idea I have.