The NES version of Metal Gear butchered the storyline of the original version by cutting out important plot elements and adding new ones that were never in the MSX version and contradict the rest of the storyline in the series. To make things worse, Kojima was never notified of these changes. They were done without his permission.
Think of it this way. Suppose you write a best-selling novel, and when it gets imported to another region, a different author is given free reign to change characters, cut out major plot elements, and change the storyline as they see fit. You as the original author has no say in the matter, and you are forced to watch as something that you created is butchered and changed.
With MGS:Rising, Kojima has given his permission to Platinum to work on a storyline that fits the game. And since it takes place after MGS4, there is plenty of freedom to work on a new plotline. Think about it, the world is not going to suddenly be a peaceful place just because of what happens at the end of MGS4. Yes, the ending of MGS4 does close the chapter on the storyline that started in MG1, but it does not mean the world is going to be a world filled with happiness and sunshine. Look past all the main characters, and you have a world that has just been changed radically.
Maybe something happens to Raiden? After all, its implied in the ending of MGS4 that it will take some time for the world to recover from the influence of the Patriots. Maybe the storyline in Rising covers a group that appears to fill the void that the Patriots left. Has Kojima even stated how long Rising takes place after MGS4?
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