Veterans who plays "The Windwaker" will recognize a mix of Wind and Earth Temples in which Toon Link teams up with both Medli and Korok to deal with the major puzzles leading up to both bosses of the two temples. But here, it's much simpler than that with a high price: Cia's life is on the line as she's important enough to be protected.
Four the bases!
On each corner, you have to conquer the bases because of the lightning that's attacking your army. With King of Red Lions and Tetra, use the hammer than the hookshot to get to the base. On particular, use King of Red Lions to attack the messenger on the left first before attacking the base.
Two the monsters!
Once the corner bases have been overtaken, Gohma will show up on the south west and Manhandle will show up on the south east. Also, Cia's Allied Base would also be attacked later on at the same time. First, get Link and Lana at both ends to use the hammer and hookshot so the team can team up against the two monsters. Deal with Manhandle first since it requires the boomerang. Gohma has to be hit by arrows in the eye and once both monsters have been dealt with, retake the base stop the lightning base. If Cia is in dire need of help, at least leave one with her so she can stay alive as she's key for the finale. If you have the option, take the two middle west and east base for treasures and slowing the enemies down.
One for Phantom Ganon!
Once everything has been dealt with, Phantom Ganon will come out of his base. Command your team on Phantom Ganon. Your team will automatically use their powers together. Attack him once the cutscene is over. Cia would be out of action so use special and spirit powers from every character and completely attack his weakpoint as much as you can. You'll reach one more cutscene to signify the end of this exclusive adventure.
All's well that ends well
The cutscene will show Phantom Ganon's defeat. King or Red Lions and Tetra will disappears waving goodbye. Link, Lana and the good Cia returns to Hyrule Castle to meet Zelda to close the Windwaker world before Lana and Cia leaves with Lana waving goodbye. Last of all, this would not be completed without the credits! So if you're still itching to do something after the credits, that's easy! Try changing difficulties and go for more skulltullas, even the onces you couldn't get before. Also, try Adventure Mode and Challenge Mode to unlock further surprises like characters, costumes and even more powerful weapons. Keep fighting to become the number one Hyrule Warrior!