ITEMS TO GET: Gold Nugget, Aquasol DX, Seal Ar

   Back on the Yggdrasil, take the helm and return to the Orphanage. Now that Billy is in your party, you can put the three books into the bookcase in the back room. It will move slightly, and you can then push it out of the way. Go through the door it was blocking and collect the B&J686 Gun from the chest. It's better than the B&JM, but you can't use it yet, since you don't have any ammo.

   Now return to the Ethos HQ, where you'll find all the priests murdered. Head north through the wire gate, then enter the door on the left (where Billy led you earlier). As soon as you set foot in here, you'll have to fight four Assassins; two short ones and two tall ones. The short ones will use claw attacks; when they say "Next turn you'll die", they won't actually kill next to turn; just use a strong attack (for about 100 damage). Fortunately, you can kill them before they ever get a chance ^_^. As for the taller (priest-like) assassins, they mostly use Seal (for about 80 damage), but they occasionally use a Net attack to paralyze you.

   Anyway, after taking care of the assassins, go all the way west down the hallway and enter the door at the end. This is the pontiff's room, which you previously couldn't enter. Go through the open doorway and descend the stairs. Talk to the dying bishop, then continue down the stairs and exit into the high-tech area. Go down the hallway and take the second door on your left (leading north). Climb up all the stairs and you'll be back in the church. Open the chest for a Gold Nugget, then go south into a room with two more chests, which contain Aquasol DX and Seal Ar. Now go back down into the high-tech area and exit to the east.

   You'll see the pontiff getting shredded by three of the short assassins; then you'll have to fight them. Kill them, then continue east through the doorway to a fork in the road. Take a left turn and follow that hallway to three doors. Enter the middle door and talk to the guy there, who is from Shevat. After the dialogue is done, go back out and enter the eastmost door to free Big Joe. Then go back to the fork and continue east. Go through the door, then turn turn north and get on the nifty-looky elevator. Ride it down. Once it stops, go north and enter the first door on your right. There will a lot of plot exposition. Afterwards, go outside and there will be more scenes. Follow Jessie north into the door at the end of the hall. Stone's Gear will take off, and there will be a bunch more scenes in which you are introduced to Krelian, another one of the game's principal villains.