As far as the timeline goes, this takes place after both Zant and Ghirahim have been defeated and Cia needs a place to call her own. However, Ganondorf is there first, coming from the south of the map. This is the only instance in which Lana helps you defeat him before Cia's tale comes to an end. You can only choose between Cia and Volga in this last level.
Two Gohmas and the Manhandle crisis
Your warrior will start in the middle of the map. Attack the middle first before going to the west, and keep arrows at the ready. Like before, shoot the eyes with arrows before attacking with special and spirit attacks, cutting the monster eye's health down. Do the same on the east base where Cia or Volga should be, depending on who you chose.
Manhandle will show up and attack your base from the south west where you attacked the first Gohma earlier on the middle west base. Get your boomerang ready and attack as follows: When the heads change color to a natural green, throw your boomerang at it. There's a random chance of one to all four heads being disabled. Then attack as soon as the monster plant opens up. Keep going until the monster boss it's defeated.
Icy Poes and Wizzro's betrayal
Wizzro will suddenly betray you and start summoning Icy Poes to attack your base. Also, your allied warrior will retreat after going to Ganondorf's trap. Either take down the Icy Poes first or attack Wizzro so he'll stop summoning more ghosts; no matter which task you handle first, the stage will become easier.
Go to the north and make sure that no more monster officers have attacked your base, as it's easy to get stuck on one task while your allies are trying (and failing) to keep the enemies from coming through. Clear up anymore problems before the gates open; it's time to take Ganondorf down.
Lana's rescue
Lana will show up at the Fairy Fountain in the middle alongside one of your allies, returning from their absence. Ganondorf is invulnerable due to his dark magic. In fact, his base has a barrier that makes him powerful and only Lana can dispel it.
Simply protect Lana and cut down any enemies along her path until she reaches the Enemy Base. Once the dark barrier magic has been dispelled, attack Ganondorf to end this level once and for all and have Cia dismiss Lana once more.
This should explain Lana's decision to go her separate way and call on her allies - Link, Impa, and many more - to help end Cia's quest to take over Hyrule.
Remember to keep updating your warriors and increase the difficulty level to obtain more medals and experience. This should make your job easier should you choose to go through Cia's Tale over again.