I'm having trouble with the merchant guild string. I tried the empire string and everything seemed to work great but when I get to the mission in the merchant string where I have to defend zaxted starport from the empire ships only one ship shows up plus I see these little grey dots on my map they kinda look like the dots of disabled ships except there is nothing there.
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Welcome to the boards, darth42vader.
A bit more info will help us help you better.
What computer system are you playing on?
Do you have any plugins, other than E2, in the plugins folder?
Have you used that pilot file with other plugins previously to playing E2?
Do you have a recently saved pilot file you can go back to and retry this mission? If not, it's a good idea to save your pilot files every once in a while. That way if you realize you need a bigger ship or escorts, etc, for a mission, you can always abort the mission, then upgrade. I do this when trying out ships to buy so instead of losing credits every time I buy a ship I use a recently saved pilot file.
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Hm, I recall those weird ghost dots on the radar from some EV/O plug too. Possibly Frozen Heart. IIRC, if you went to that spot on the radar you could shoot around and eventually see your shots impacting the object and pushing it around. Very strange. In my case I don't think it was important for any mission so I didn't worry too much about them. So... I can't really offer any help I'm afraid.