as a matter of fact - we just had the kick-off for the 3rd Klingon specific episode today - and part of the mission required you to launch a sneak attack on the Utopia Plentia shipyards above Mars.
So yes - Klingon specific episodes starting in Season 2 will introduce a Klingon Faction specific story arc to the game.
Comments
I doubt it. I'm guessing it will be just like any other quest that takes you to a system location with multiple options. You'll see one button for normal entry and one button for your specific mission.
The mission over mars will probably be instanced separately from the complete Sol System map (the latter replaces the current Sol space instance, I assume).
http://forums.startrekonline.com/showthread.php?t=155026
Image as below:
http://stevewalsh2.pwp.blueyonder.co.uk/BeamUI.jpg
So in this context you'd be given a pop-up of the starsystem's layout with a number of valid warp-in coordinates [justified as the closest position the ship can safely warp into the system].
I dont think so, but it was promoted here.... http://www.startrekonline.com/upcoming_content