After you help Jack of Alltrades, you should go south to find out what is happening in Porth Llaffan.
Visit Porth Llaffan
Porth Llaffan is in the southern part of Newid Isle (the island where Alltrades Abbey is).
When you arrive in Porth Llaffan, go to the beach and talk to the pink-haired girl looking out at the sea. When you walk away, a cutscene will begin. (If this doesn't happen, you may need to rest in the inn until daytime.)
After the cutscene, if you talk to Jona, she asks you to visit her house this evening. So go to the Inn and choose to Rest, then go into the easternmost house of Porth Llaffan and talk to Jona. After she leaves, go outside and go to the west side of town. Enter the big house there. Go to the left side of the house to start a cutscene. During the cutscene, Jona will ask you a question. You can answer however you want.
The next day, nobody knows where Jona is. You need to look for her, but before you go, you might want to buy supplies. Also, read the books in the Mayor's house to find some Alchemy recipes.
When you are ready to move on, talk to the mayor's son, who is standing by the gate at the northwest side of town.
Outside Tywll Cave
After you go through the gate, you will be outside. Go west to find a beach area. Go to the southeast part of the beach to find a red chest that contains a seed of magic. Then go west, and go past the cave entrance to find a blue chest. Then go back, and enter Tywll Cave.