Ending and Continue playing

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I have finished the main story line and chose the continue playing option. I was re-loaded into the game at a previous point only to find Johnny still there, popping up every so often and the Nocturne OP55N1 mission in my list.

So there is no opportunity to play the game after 'finishing' it without Johnny and the main storyline?

Why even have the option to continue playing?
 
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