How to Unlock
To unlock the last story, you need to complete all of the endings by following good and evil paths, once you've defeated all of the final bosses such as Black Doom, The Egg Dealer, or the GUN commander and Sonic, the last story will be unlocked,if its still not unlocked, it means you missed some endings...If so, go again over the whole story and remember which paths you took and which ones you forgot to take, now after seeing what you missed or after unlocking the Last Story, select it, and the cut scenes of the real truth from shadows past shall appear one by one.
After the first 4 cut scenes, you go to the last stage named "The Last Way" which is the longest stage in the whole game, as the other stages, it has Secret Keys you can collect, the only difference is that in this stage there are constant Dead Ends, and you'll need to use Chaos Control to proceed, but this isn't too much of a challenge, since you can defeat lots of aliens to gain chaos control powers, once you got your gauge full, use chaos control, keep going, but remember, theres a time limit of just 10:00 to clear the stage, if you run out of time, you start again.