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the story mode is made up of 4 different story lines 1 for each force wu, shu, wei and samurai warriors. the overall story is that they team up and kill orochi other then that they differ ever so slightly but that contributes very little to the overall game experience
Free mode lets you play any battle and any characters you have unlocked in story mode. Story mode limits you to a particular faction until you clear the story. After you complete a story mode, you can play any of your unlocked characters in that story mode. This can be helpful for unlocking more characters (which must be done in story mode), efficiently farming weapons, etc.
~ http://rydain.org/ ~ "A little nonsense now and then is relished by the wisest men." -Willy Wonka