You start the game in a small bedroom in the northern corner of Fort Emergence. You will be able to use this room throughout the game to rest. The first thing you should do is collect the items from around the room, giving the different items to the characters you think need them. Don't forget to look in the dresser and chest for more items.
The next room on the same side of the hall is a character storage room. You can store characters here if you don't want to use them, or if you want to pick up NPC's, but don't want to delete the characters you already have. There's also some coins in the chest which you can steal.
**NOTE: Stealing is only bad if you get caught. I find the best way to make sure I don't get caught is to shut the door of the room I'm stealing something from, and press the talk button. If I get a message that there's no one there, then I know it's alright to take the item(s).**
In the last room on that side of the hallway is an energy potion in a dresser. You'll have to steal it too, and you'll need either the Unlock spell, or the lockpicks you picked up in the first room.
On the other side of the hall is a dining hall and training room. In the dining hall you'll find Gordon, who doesn't really do anything, but feel free to talk to him. You should use the training room if you have any skill points.
In the next section there's nothing but two barracks with nothing in them, and a cat that you can commune silently with.
If you go out the doors to the west you'll find yourself in the main courtyard of Fort Emergence, and if you go to the south you'll find yourself in a passage leading to the Magician's Offices. In the main part of the Magician's Offices, which also double as a laboratory, you'll find Mazumdar. A little bit further into the game she'll give you access to two tomes which teach you Far Sight Lv. 2 and Move Mountains Lv. 2. The door at the end of the laboratory leads to the greenhouse. There's nothing really there. If you go through the other door in the greenhouse you'll find yourself in the library. Berra stays there, and you'll need to bring him evidence after you complete each major quest.
Down the hall from the Magician's Offices is the Monster Pens. You'll find Eva here. She heals you for a small fee, and she'll also tell you about animals you come across.
Now head out into the main courtyard. At the northern end of the courtyard you'll find two people wandering around. Thereza is a spy for Covert Operations, and she'll give you a quest to recover some lost papers. Habecker is a sage who's wandering around, and he'll identify your items for you. It's better to use him than Levy. To the right of the northern gate is a secret area with a Cavewood Crossbow, some stone bolts and some dried meat. You have to cross over some lava to get to it though, and a trap with a difficulty level of 10. This means you need to have at least 10 points in tool use skill. To the left of the gate is another secret area, where you can get some coins, and a Bolt of Fire Spellshard, but you need either a piercing crystal or Dispel Barrier Lv. 2 to get them.
Now go down to the south end of the courtyard. You can go explore the graveyard in the southern corner if you're feeling ghoulish, and just at the entrance to the graveyard is a Rough Diamond lying on the ground.
If you go into the doors to the south you'll find the kitchen directly to your right. Elisa will give you one loaf of bread per day, and you can pick up three more from the pantry to the right of the kitchen. Now go into the dining hall and talk to Commander Johnson. He'll give you a quest to clear out a Bandit Lair, and he'll be kind of rude to you too.
On the other side of the hall is a row of barracks. There's nothing in the first two, or rather there's nothing in the first one, and there's witnesses in the second one. The last barracks however, on the far end of the hall has a secret closet in the southern corner. You can pick up a couple scrolls in there.
Now go along the hall to the west and you'll go through a very short passage into the main storage area of Fort Emergence. The barrels and crates at this end of the room are all empty, but you can check them anyway. I have been known to make mistakes.
There's two rooms on the Eastern wall. One is the water reservoir, and the other is the office of Captain Ko. He'll tell you where you can pick up some more stuff, and where you can store your excess items. There's a little room off the side of his office with a Fine Waveblade, but again you need either a Piercing Crystal or Dispel Barrier Lv. 2 to get to it. You also need Unlock Doors.
As you leave Ko's office you'll notice a large number of crates and barrels, and some of them have some very nice items in them. Remember what I said about it's not stealing if you don't get caught? Well, fortunately you can push barrels and crates around. Go down to the end of the room, and to the east and you'll find your storage room. Open the doors and then go back and check the crates and barrels. Whenever you find one that has something you want push it into the storage room. Once you have them all collected in there, go in and close the door. Press the talk button to make sure a lizard hasn't snuck in. In this game even the pests are finks. You can now loot the items from the crates and barrels at your leisure, and make sure to pick up any of the items that were already in the room if you can use them.
Once you're done here it's time to go meet Levy. Levy will do many things for you in this game. You can go to him once a day and collect your allowance of a measly 25 coins, he'll give you your reward whenever you complete one of the major quests, and he'll also buy and sell you items. Due to a bug in the program, whenever you sell something to Levy he will then have an unlimited supply of it, so it's best not to sell him things unless it's something you're going to want more of later. Magic crystals, good ammunition for weapons (ie. Blessed arrows, fine razordisks, etc.), elixirs and brews are all good items to sell to Levy. That way you can be sure you'll never run out of a place to buy them.
Now it's time to go to the offices of Unspecified Services. The first room on the right, and the first two on the left are empty. The second room on the left has Flanagan in it, and the last room on the left has a map to the Bandit and Goblin Lairs. The last room on the right is Anaximander's office. Pay attention to what he says, and when he's done talking go in and ask him a couple questions. Pick up the two maps he offered you and look at them. You can leave the Anaximander Note you picked up in the bedroom here, as you won't be needing it anymore, and it's best not to clutter up your storage area with too much stuff, as it will only hold a certain number of items. I believe it's something like 200, which sounds like a lot, but do you want to risk losing a really good weapon for a piece of paper if your room gets to full?
Now it's time to leave Fort Emergence. It's best to start with the Goblin and Bandit quest, as Anaximander suggested, since you need to build up your levels a little bit. Follow the Bandit Map to begin the adventure, and talk to the soldiers who stop you when you first get outdoors whenever they approach you, as they'll give you one point in reputation if you tell them about the surface once you've been up there.