Leck Mine, 1st Floor

Once you're back in Parm, have dinner with Lilly, then head over to the docks and talk to the sailor. There's a ship coming to town in two days and to get the passport, you need to talk to somebody in the Underground Cafe.
You go to the Cafe, but the owner's looking for a key. She'll tell you that her son has it and that he's down at the docks. Go down to the docks and talk to the people till you find the one you want and he'll give the key to you. Return it to the owner of the Cafe and she'll ask you to come back that night. It'll turn into night almost immediately. Visit the Cafe and talk to everyone. You'll learn that the man with the pass is Java and that he's at the Leck mines.
If you talk to the owner of the Cafe, you'll learn that Java had left his wallet at the Cafe. Offer to return it to Java as you are going to the Leck mines to meet him.
Then go back to Lilly's place and have dinner or meet with Mary, if you've decided to do the side quest. This quest seems to get you nothing important but you can find her brooch for Mary - it's near the Baal museum.
Go to the train station, talk to the man next to the gate, then go on through and go on a train trip to the Leck Mine
Go visit Java, who'll rage at you, then calm down. He'll lead you to the mine entrance and becomes a save point afterwards.