Instructions
Return to Rougeport with the Diamond Star, and speak with Dr. Frankly. She will tell you that the Emerald Star is located in the Great Tree.
Enter the Rougeport Sewer, and travel past the Underground Shop to the room where you got the Black Key. Here, you'll encounter a little spritely creature that will guide you to the Boggly Woods where the Great Tree is located.
Follow the path through the Boggly Woods until you reach the Great Tree. Along the way you'll encounter both random enemies and the Siren Sisters. Heal yourself as necessary.
Talk with the sprite at the base of the tree, and he'll tell you that you need to speak with Madame Flurrie to get into the tree itself.
Continue following the path until you find her abode. Inside is Madame Flurrie, but she refuses to help until she gets her necklace back.
Walk back towards the entrance of the Boggly Woods until you encounter the Siren Sisters again. Battle them to recover the necklace.
Return to Madame Flurrie's mansion to have her join your party.
Take Flurrie to the Great Tree, and have her use her field ability by the door. After a brief cutscene, the door will open and you'll have access to the inside of the tree.
Climb the tree until you reach the top, where you'll discover both the Emerald Crystal and a boss battle. After defeating Magnus von Grapple, the second Crystal Star is yours.