Last night I was playing the game and was on Nar Shadaa. I did the mission where you have to fight the red eclipse who took over the Ebon Hawk. I completed this mission. Later I get the cutscene again that shows the red eclipse thugs taking the ship. I go to the ship and the thugs talk to me, I fight them, go to the ship and it acts like I'm fighting the thugs. My party members are with me on the ship but there is no one to fight. I didn't think much of it and I continued with my game and finished the primary objectives on the planet but it is still doing this. I can't access anything on the ship so I can't leave the planet. I should mention that I have the "Restored Contend Mod" and the "Ultimate Saber Mod" in the game. I also have the "Save Editor" I've tried setting the journal entry back hoping that it would restart the mission and I could fix the problem but I've had no luck. If anyone can give me anything that could help that doesn't require starting the game over I would greatly appreciate it.
I have had the same problem I also have the restored content mod which I think is what is causing the problem. If you have KSE you can go into the numerics and change the number next to the red eclipse to 0 and that should fix the problem.