Map: Valley of Seers
Recommended Element: Light
Heart Container: Link
Heart Piece: Midna
Skulltula: Defeat 1,000 enemies
Head to the nearest keep and capture it. Zelda will then discover the East Sanctum and will instruct you to capture the sealed sanctums, marked in your map. Your allies will make their move to the nearby Keeps. It's up to you what Keeps you want to capture; wether you'll travel to the east to assist Zelda or take care of the Western Sanctum yourself.
The Dinolfos enemies here increase the morale of their troops so expect them move in to attack your captured outposts and Keeps. Defeat any of them that you encounter along the way to make your job easier. Keep yourself busy; after capturing a Keep, move towards the next. You also need to keep an eye to your allies' HP. Go to their rescue whenever needed.
Cia will send powerful units towards your allies. They won't arrive immediately so make sure to capture the Sanctums. Cia will also continuously power up her units by boosting their morale. The last Sanctum is located to the south. Once Lana finds it, head there and capture it.
After successfully capturing the Sanctum, regroup with your allies and reinforce their positions by repelling any attacks towards them. Because of the capture of the three sanctum's Cia's army will be weakened. This advantage is short-lived since Cia will open a Gate of Souls to summon reinforcements. Fortunately, there's a fairy fountain nearby.
Head to the fountain and so you can activate the magic circle to summon the Fairy. Before you can reac hthe fountain, two Dinolfos will move in to take over the West and Eastern Keeps/ Sanctums. You can intercept them. Volga will also advance towards Zelda in the fountain. You can ignore him for now and just proceed in summoning the fairy.
After luring Volga to the fairy magic's area of effect, you need to defeat him in battle. His attack patterns are still the same, though he'll be a bit tougher this time around. If ever you find yourself in a pinch and low health, there's a destructible boulder in the vicinity, northeast of the fountain's entrance, that contains a red jar with full HP recovery.
After defeating Volga, the main temple's gates will be open. Cia's remaining forces will also attack your strongholds so intercept them and prevent them from capturing your bases. Once done, make sure you're fully healed before fighting off Cia.
For the first part of the battle, Cia will be able to summon Dark Links to attack. These shadows will disappear after attacking and they don't seem to have the ability to move on their own. This move will reveal her Weak Point Gauge. Remaining close to her is risky but should you be able to do it correctly, you can attack her while she's summoning the Dark Links since her blind spot is around her at very close range.
She can also fire fast dark projectiles. Don't bother blocking these since they can break your guard instantly. If you see her hovering and dark circles start to form on the ground in front of her, quickly break your attack and dodge back. If you're able to evade this successfully, this is another move where Cia will reveal her Weak Point Gauge.
Once she's critically injured, she'll create three more clones of her, with the same strength, weakness, attack pattern, with their own health bar. Even if you defeat the original, the clones will still fight independently. Lobbing bombs at them and keeping yourself at medium distance seems to be effective since you're able to deal damage (albeit small) using the bombs but if you time your throw right after Cia's specific attacks, it's possible to damage their Weak Point Gauge, and send them flying to you. You can also air juggle them if you time your attacks right before they hit the ground. If possible, use your SP attack when the Cias are close together.
After this scenario, you can now battle as Ganondorf. The 8-bit Wooden Sword will also be unlocked.