Head back to the Conde Petie Mountain Path and once again select the left trail at the split. Head back towards the Iifa Tree and enter, you should probably save at this point, since you haven't been to a save point in awhile. You can call the moogle on the world map by pressing the square button. When you enter the Iifa Tree Dagger will spot Kuja's silver dragon flying overhead. You will have the option to Change your party members again or go to the menu. Either rearrange your party members or just keep your current ones.
Proceed into the Iifa Tree and once again follow the branches until your party reaches the end. Watch the scene and eventually you will be able to choose how you want to organize your party... yet again. Select finish when you are ready, Queen Brahne will show up on her boat. Kuja will summon Mistodons, they are not very hard to kill. Once you have killed the first batch, Kuja and Brahne will continue fighting.
Dagger runs off and another Mistodon attacks. Head down the roots and continue moving, more Mistodons will appear and they will come after you. As you move down more Mistodons will chase after you until you reach the bottom. You will find Dagger and she will acquire the Aquamarine, which will allow her to summon the Eidolon Leviathan.
Watch the events and dialogue, once they are finished the second disc will come to an end.