Cia’s story includes five missions in Legends and the Definitive Edition. On the 3DS, entry unlocks after the original Ganon finale; on Switch it is already accessible after Cia’s defeat in Valley of Seers. You then follow this storyline from the Eldin volcano through Hyrule and the Shadow Realm to the final battle against Ganondorf.
Eldin Caves: Ring and Bombchus
Search for the ancient ring by capturing the two marked keeps to the north. The clue then leads you to the crystal cave in the northeast. Go through the winding entrance and take the ring. Volga cannot be finally defeated in the following early encounter. Instead, capture the four keeps occupied by his troops to the west.
As soon as the three Bombchus appear, you interrupt the conquests and destroy them on the way to their goals. Then return to the missing keeps. For the final battle you have to defeat Volga and Wizzro. The additional King Dodongos that appear become particularly urgent when they threaten the Crystal Cave as your base. Instead of attacking in the middle of Volga and a large monster, keep the fights spaced out.
Hyrule Field: Lana, Impa and Zelda
With Volga and Wizzro you conquer the first accessible keeps and intercept the Goron captains in the east. They are not allowed to reach the defensive keep unhindered. Then secure the eastern keep to open the path south to Lana.
Defeat Lana at the Fairy Spring and then Impa in the west. If fast enemy units are announced during this time, intercept them near their starting position before they spread across the map. Finally, Zelda appears in the southwest. Bring both controllable characters close to her and defeat her. With Volga you can also get a Piece of Heart from the Conquest Chest at the Fairy Spring.
Palace of Twilight: First Twili Midna, then Zant
Work your way across the northern keeps with Cia and Wizzro. To access Twili Midna and Zant, you must first conquer the keeps in front of them. Zant cannot be finally defeated at this early stage. Therefore, go to the northern throne hall and first defeat Twili Midna.
Interrupt the advance as soon as Volga is threatened by Fire Gibdos in the southern area or strong troops want to reach the southwestern base. Distribute Cia and Wizzro to the vulnerable sites. You can then finally attack the Zant that reappears. He wants to escape to the fairy spring in the southeast; catch him in time.
When the middle gates close, you need Agitha’s key to reconnect the card halves. Defeat them south of the throne hall. Argorok in the northeast is an additional danger, but not a necessary detour if you can already safely defeat Zant. Defeating Zant ends the mission.
Skyloft: Distribute three characters along the paths
You start with Cia, Volga and Wizzro in the northwest of Skyloft. Capture the southern entrance keeps and defeat the Imprisoned behind the bridge. You open his white toes first; Only then is the fallen body the right target. Meanwhile, send a free ally to Ghirahim and take him over after the first boss fight.
Defeat Ghirahim and secure the three marked keeps. Intercept the newly emerging conquering forces before they undo your work. You can also accompany a supply soldier to the knight school. Fi in the southeast is the completion destination; if you want to kill the Side Quests, only defeat them afterwards.
Valley of Seers: Wizzro’s Betrayal and Ganondorf
Defeat the two Gohmas that threaten the East and West Keeps. After her beam attack, the bow hits the black eye. When Wizzro betrays you, you find him in the west and defeat him. The Ice Nighthawks on their way to the northern base then have priority before a longer fight against Manhandla.
Once the base is secure, finish the fight against Manhandla with the Boomerang against the green heads. Ganondorf appears in the south. Accompany Lana to his headquarters to remove the protective barrier and intercept the new strategists along the way. Only then do you attack Ganondorf with your assembled characters. With his victory, Cia’s storyline is complete.