I just finished the Goner plot... but

[The Rogue Trader]

dont seem to get the UFJD after returning to the Ozias. Does the ship i am flying need to have a regular JD and do I have to be in a commonwealth ship ?

[Fulgrymm]

It's not something that shows up in your ship's cargo hold, but rather becomes part of your character's inventory, like the police licenses. This way you'll always have it with you, regardless of the ship you're flying.

[Ragingpoo]

It will always be available to you regardless of ship, to use it, either bind it to another key via control menu, or access via navigation menu from the side bar