[ShivanSlayer]

I beat the campaign for the 5th time, but several ships, namely the Hyperion class cruiser Pallas, did not show up in the final mission despite me protecting them.  I distincly remember on my first playthrough that the Pallas showed up.   Also, despite 5 playthroughs, alternating branches each time, I only have about half the medals.  Are half of them only available in part 2 whenever that comes out, or am I missing something

[Goober5000]

The other half of the medals will be awarded in Part 2.  All of the medals in the medal case will be awarded, at some point, over both halves of the campaign.

The Pallas is indeed supposed to show up in the final mission.  Can you upload your checkpoints?  They should be in %APPDATA%\HardLightProductions\FreeSpaceOpen\scroll\data\scripts.

[ShivanSlayer]

Can't figure how to get to them. At least I beat the mission, though it was hard

[Goober5000]

Just paste that path into Windows Explorer.  Or at least paste this part, as the Scroll folder may have a different version: %APPDATA%\HardLightProductions\FreeSpaceOpen\

[ShivanSlayer]

Here is the stuff in the scripts file

[attachment deleted to save space]

[Goober5000]

Sorry for the delay; I finally got back to this.  According to your checkpoints, the mission didn't save the Pallas so it could be restored in the next mission.  Not only that, the Pallas wasn't saved from the previous mission (the last mission in the ISF branch) either.  On it's own that strange, but what's stranger is that if the Pallas was in Irkalla Passes, and it departed, then it should be in the next mission, regardless of whether the save file worked.

I found a few fixes I could apply to the mission, but nothing that appears to explain the problem you saw. 

[ShivanSlayer]

Like I said, I at least managed to stop the Irkalla. It was just MUCH harder