The Root can be found in Gramor. Warp over there and switch Mogu to the front. Head southwest from the mole town where you'll find an odd-looking plant. Dig here to find a Root.
When you have that item, Warp back to Carmen and speak with the doctor. He'll use the items to make the Tonic. Once you have it, Warp all the way to Tunlan and use it on Nina. Finally, she'll remember just who you are and rejoin your party. Now, onwards with the quest.
Learn more by checking this Breath of Fire - FAQ/Walkthrough from Gamefaqs.com.
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