**This will be the last walkthrough in which I mention items dropped by creatures after you've killed them, unless it's a special item. You should always check after each battle to see what's been dropped, since you'll probably find you get most of your equipment this way, as well as it being your main source of income by selling things dropped during battle.**
Upon first entering the Agate Tower, go into combat mode before stepping from the entrance into the hallway. There are some archers in a little guard room just down the hall. You can't reach them, so you'll have to use missiles and spells to kill them.
Once you've dealt with the archers go around this room to the north and enter the door. Again, be prepared for battle. There's a bunch of slimes in a pit in this room, and I find it's usually easier to again use distance attacks rather than go all the way around to the stairs on the other side.
Enter the room to the east of the pit and you'll be confronted by two bandits and a wolf. I usually don't even bother to enter combat mode to deal with them. The door to the north leads to the room that had the archers in it. You might want to go see if they've dropped anything you want. If you have an archer keep an eye out for the Yew Bows that are sometimes dropped in the Tower.
Now go back into the room that had the slimes and through the door to the south. There's some bandits and archers, and an Apprentice Mage in here. There are two doors leading to the south. The one on the western side leads to a couple crates with a few useful things, but you need either Dispel Barrier Lv. 2 or a Piercing Crystal to reach them. The room to the west has a secret passage against the Western wall. This leads first to an empty room, and then to outside. Once you're outside the secret door will lock behind you, but go towards the trees to the north and you can pick up quite a few coins in one of the trees.
After you get the coins re-enter the Agate Tower and head back to the room where you fought the Bandits and Wolf. There's a trapdoor leading down to the Lower Level here.
Upon entering the Lower Level via the ladder you'll find yourself in an area with a lot of alcoves containing Goblins. Clear out the area, paying attention to what the Goblins drop, as they occasionally drop scrolls. Once all the alcoves are cleared head towards the Northeast corner. You'll have a run in with a few slimes outside a set of doors, and there will be a passage leading off to the north. Go up the passage to kill a few more goblins who are farming some mushrooms. If you need food, don't forget to pick up the mushrooms.
Head through the doors and you'll find yourself fighting a few bandits and archers. Once they're disposed of go through the doors to the west and kill a couple more bad guys. There are two rooms leading off to the west. If you check the desk in the room to the North you'll get some information on something called the Slime Pit.
Now go back into the main room and through the door to the south. There's an archer and a bandit guarding this passage. The hall itself forms a sideways U. In the center is the water reservoir. The two storage rooms leading off to the west have a few items worth picking up.
Go out the door at the end of the U, leading to the west. If you go around the corner you'll find another ladder leading up to the Upper Level.
Right outside the trapdoor are a few slimes in another pit, and two doors, one leading north and one leading west. Go through the northern one first. This is the Tower Kitchen. There are a couple Bandits and an Evil Priest in here, as well as a wide variety of food items. Go north again, through the curtain, and deal with the bandits in this room. Now go back to the room you came up in and go through the door to the west. This leads to Bojar's Throne Room. There's a lever beside his throne, and if you pull it it will disable some traps in the tower. You can now ignore the message that you get when you first try to step onto the orange sections of floor on this level, and the portcullis will no longer trap you if you use the stairs in front of the entrance.
You have two choices of what you want to do now. First, you can go back down the ladder you just came up and go through the one remainind door leading off the U-shaped hallway. This will take you to a few crates with some food and a boat. Use the boat to go as far south as you can and you'll find yourself in a room with a Slime Spawner, which look like little green pits in the ground. Use distance attacks to kill Slime Spawners, as they'll produce a field which puts you to sleep as soon as they're attacked. Fire spells are particularly effective against them. Alternatively, you could have gone down the stairs in Bojar's Throne Room, which would have taken you right into this room.
Once you've killed the Spawner go through the door to the west. There's a couple Giant Spiders in this room, which appears to be an unused kitchen. Once you've killed the spiders check out the northeast corner of the room for a secret passage. There's another room at the end of the passage with a chest and a book. The book teaches Forcecage Lv.3 once you've learned the spell at Lv.1, and the chest contains some coins.
Go back into the kitchen and walk south, watching the northern wall for a door. This door leads out into a room with a Guard Worm. Once you've killed the worm check it's nest for some more coins and a Silver Ring. Follow the passage leading off this room to the west and you'll enter the Tower Temple. You can use the Ritual of Sanctification on this altar once you've gotten the ability, so remember that it's there.
Head back into the unused kitchen and go towards the southwest. You'll enter a room with several glowing runes. Bojar will summon a few slimes and then flee the room. Kill the slimes and then check the wall in the Southwest corner for a secret passage. There's some pillars in here, and two barriers. These are only Fire Barriers, so you can walk through them if you don't have the spell Dispel Barrier or any Piercing Crystals, but they'll damage you. Once you can see Bojar standing against the western wall of the room start attacking. Once again, distance attacks work best because that gives him less time to summon creatures. Once he's dead check and you'll see he's dropped a Robe of Magery, a Healing Elixir and sometimes an Ice Lances scroll.
Go through the locked door to the west and you'll be in Bojar's bedroom. Read the book to learn the location of the Slime Pit. Check the bookshelves for a Bolt of Fire scroll and a Call Beast scroll, and there's a ruby in his desk. Once you're done here exit the tower and head off towards either Colchis, which is an optional part of the Slime Quest, though highly recommended, or the Slime Pit itself if you choose not to get the items from Colchis.