The post should actually be in the thread
Fall of the Rising Sun Ultimate. This is the "beta" release thread, but we can manage from here. Can you zip-up the Save folder data, post it to a sharing site, and PM me a link? I would like to see the "CareerTrack.upc" file in the newest Save folder. There will be a line in there with "PlayerCurrentObjectives=IDxxx", with the "xxx" representing a number that points to a file named in the PatrolObjectives.cfg file. With that info, we can look at the file, and see if the mission is the cause of your troubles, which it sounds like it is.
You boat is assigned the next mission file upon your arrival back at base, so once that is assigned, it gets stuck in the game's Save folder data, and you cannot get passed that if you cannot complete the mission. A possible fix is to change that number to a know-good mission assignment, so that the game can finish loading. Then you can go do what you want, or follow orders... There might be another way around it, but it is based upon what the info in the Save folder is.
Out of curiosity, what was the approximate date you came back into port, or else the approximate date it said you would sail? Do you remember the text of the orders you received, as well as the Objective listed near the bottom, or did the game crash before it could take you that far in? Thanks for any more info you can supply. Sorry for your troubles with that.
btw, which version of the mod are you using, and can you use JSGME to generate an activated mods list?