JK is the "Hero" of this game. Think of this game like the original trilogy, the JK is Luke Skywalker and the SW is Darth Vader (without the father/son thing). Both of them are connected to the Emperor (Vitiate/Sidious), one is his 2nd in command (Vader/SW), the other looks to defeat him to bring peace back to the galaxy (Luke/JK).
If you have played the SW story, it will be cool to see the story of your arch-nemesis in the making play out.