Map: Temple of Souls
Recommended Element: Light
Heart Container: Impa
Heart Piece: Fi
Skulltula: Defeat 1,000 enemies
This story scenario is also limited to Link only. (After completing this scenario for the first time, you can use any character afterward) Make sure to get him some new badges and have a mixture prepared if you have spare Materials at hand. Link will also get the Master Sword, which has an outstanding attack power and a skill that only unlocks after defeating 25,000 enemies.
Head inside the Temple and take out the enemies. Your immediate objective will be capturing the Magic Keeps marked in the map to sever their connections. Go to these Keeps and clear them off enemies. Shortly after, ReDead Knights will appear and advance towards Zelda. These ReDead Knights will keep coming even after you defeat them unless you sever the connections of the Magic Keeps.
After severing the connections, the Sorceress' Room will be opened. Head there and you'll have to defeat the Dark Link Cia summoned. This dark version of Link has the same attacks as him so you just need to circle around it with your shield up and counter attack as soon as Dark Link stops its combo. Once you're able to stagger it, don't hesitate to be more aggressive. Its Weak Point Gauge appears shortly after finishing its attack and destroying the gauge can be done in a few hits.
After defeating the first Dark Link, more of its clones will appear. While engaging one of the Dark Links, Ganondorf will arrive with his own forces to join the battle. Proceed with defeating the other Dark Links then engage Ganondorf's forces. After defeating two Dark Links, the other two will temporarily vanish from the map. Watch out where the third one will reappear and rush towards it.
After defeating the third Dark Link, the entirety of the Hyrulean forces will fall back to the West Garden. The fourth Dark Link is found in Cia's room. Head there and defeat it. The trap in Cia's chamber will close all doors. After defeating this Dark Link, more of its clones will appear. Just when you're about to fight them off again, a cutscene will play.
Once the cutscene's done, it's now time to fight off Ganondorf's forces and reclaim any lost Keeps. While you're at it, Cia will summon more monsters to join the fray. Don't overextend yourself, just defeat the enemies in your immediate area as they come. The rest of your army will march towards the Western Rose Garden to escape. Stay along their path and defeat all the enemies that may block off their escape. While you're protecting them, keep an eye on Zelda's location. She'll be cut off and will be surrounded by Ganondorf and his army. Quickly dispose of the enemies near the escape point then quickly go to her rescue.
To finish the mission, you have to defeat Ganondorf himself. Since the battle is pretty intense, it's hard to keep track of Ganondorf's moves. Like the other small bosses, his Weak Point Gauge appears after his special attack/combo. Since there are leader enemies in the midst of the battle, don't hesitate to use your Focus Spirit and SP attack to deal with the hostile crowd quickly and effectively.
Keep defeating enemies and you'll most likely find Bomb power ups. Use this to your advantage since an upgraded bomb deals tremendous amounts of damage to any enemy, with a rather large blast radius. This is a good way to eliminate most of the enemy forces while dealing damage to Ganondorf at the same time. After defeating the leader monsters, the lesser peons shouldn't give you that much trouble. Lock on to Ganondorf and defeat him.