After Marle disappears, you should go to the cathedral to the west.
Go to the Cathedral
Go to Guardia Forest and level up until you learn Fire Whirl.
Go to the cathedral to the west. Talk to the nun by the organ, then check the sparkle.
On the Naga-ettes, use Fire Whirl. You can use Fire Whirl on three of them at once.
Go with the frog. (Default: Frog) Check the organ to reveal a secret door. Go through.
First, go left to find a couple of chests (right: Revive; left: Tonic). Then go up through the door to the left, up the stairs and through the door to find more chests (left: MaidenSuit; middle: Tonic; right: Ether). If you check the dresser, you will find the Secret Naga-ette Bromide, and you will have to fight. Finding this item will give you access to a Tab later on. Exit this room.
Go all the way up to find a chest (SteelSaber). Then go to the left, check the skull to the left to lower the spikes, and go in. Check the bucket to find a Power Tab.
Now go back out to the main hall. If you want some money and good items, go up the right-hand staircase. Skip the first door and go through the second. Open the chests (left: 100G; right: Ether), then go through the wall to the right. Don't talk to any monsters. Go up to find two chests (right: Defender; left: Speed Belt). When you try to go back out to the main hall, you have to fight. Then leave.
Go up the middle of the hallway. You can avoid the monsters here by hugging the right rail of the stairs. Go through the door. Save and use a Shelter if needed, then go up the stairs, go right, and go down the stairs. Go through the door and hit the switch on the far wall, then keep going. Open the chests in the back hallway (right: Heal; left: Tonic) and keep going. Don't hit the switch in this room. It just makes more monsters appear. When you go up the stairs, open the chest to your left (Shelter). Once you're back to where you started, go up through the door. Fight, then open the chest (Iron Sword) and play the organ. Go back to the back hallway and through the door that appeared.
Run to get past the monsters. If Crono and Frog haven't learned the dual tech X-Strike yet, you should fight until you do. Then save and use a shelter if you need to, and go up through the top door.
Run up and you'll fight Yakra. Keep everyone's HP above 50. Have Lucca use Flame Toss, or have her use healing items on people when needed. Have Frog and Crono use X-Strike until it dies. Keep in mind that it almost always counter-attacks whenever you attack.
Check both chests (left: Chancellor; right: Mid Ether), then talk to the queen to leave.
Go up to the queen's room and check where Marle disappeared to find her.
Leave the castle and go to the area of the mountains where you appeared in this time period.