Uhm, I've also been through Aftermath as well. First off, thumbs up
. Great campaign, and I really liked that you revamped it!
Secondly, in the mission where you have to scan the cargo depot in search of those documents. In the beginning 4 Elysium class transports arrive, and you later find out the Orion destroyer (sorry, I can't remember the name of it) had to meet up with them. However, the HoL sometimes starts attacking them, and if they are destroyed the Orion destroyer will not leave and the mission will never end. Could you add a directive to protect those transports? It was pretty strange the first time through because I couldn't figure what went wrong.
Thirdly, in the same mission the HoL cruiser Machus(hope that's the name) arrives if I'm not mistaken. However in my playthrough it somehow merged with the Orion, incapable of moving or anything. When the Orion left, it dragged the Aten with it and the Machus went ballistic, which was really odd. I only noticed it once, so it may just be a 1 in a million problem, but I just give you a heads up.
That would be all, again great campaign and great work!