Impa, under Veran's control, brings Link to where Nayru is hiding, in a forest surrounded by a magical barrier. Link unknowingly breaks the seal so Veran can enter. They walk through the forest and then find themselves surrounded by animals. Link tells the animals that they mean no harm. The animals leave, revealing Nayru playing her harp. Nayru notices the light inside Link, and the darkness inside Impa. Veran leaves Impa’s body and then enters Nayru’s, possessing her. Upon doing this, she uses Nayru’s power to go back in time, leaving the harp behind. Then, a figure appears in the background...
An Old Friend: Ralph
Ralph, a childhood friend of Nayru's, comes looking for Nayru and argues with Link. Meanwhile, in Lynna, things are changing due to Veran changing things in the past. Ralph blames Link for Nayru getting possessed. Impa re-awakens and blames herself. She tells Link that Veran is an evil sorceress who possesses her victims. Link finds Nayru’s harp and Ralph fights Link for it. Link uses it to travel back in time. While in the past, Link becomes a slave and loses his sword and shield to a guard. While working a man tells Link that Queen Ambi suddenly decided to build a tower that can reach the heavens, and enslaved most of Labrynna to build it. Link grabs a spear off one of the guards and tries to run away. He is stopped by Sir Raven.
Queen Ambi of Labrynna
Link fights Sir Raven, and ends up being thrown in prison. Link finds a fishing hook and uses it to break free. Link climbs the outside walls to a window, where Queen Ambi talks to Sir Raven. Nayru (Veran) talks the Queen into killing Link for treason. Nayru goes to the prison to find out that Link has escaped. Link follows Sir Raven to a river. There, he realizes that Raven helped him escape. Sir Raven then takes Link to a graveyard.
Sir Raven takes Link to a secret village that the Queen does not know about, full of people who escaped enslavement. A young girl called Roperi shows Raven a seed she is growing, given to her by Raven. Link then remembers that Raven is a knight who he has pictured in his living room, which means that Sir Raven is Link's ancestor. Raven takes Link to the village elder, and Link tells the story about the future, Nayru and Veran. Raven gives Link a weapon and they decide to go and fight Veran together.
Ralph in the present comes across the harp, which was taken from Link with his sword and shield when he first came to the past. The harp passed hands, and it eventually ended up in a shop in the present. Back in the past, the slaves start to rebel at the tower. Raven goes to the tower to sort them out, while Link goes to face Veran at the castle. Raven gives Link his sword. Link confronts Veran, but he does not know her weakness and does not want to hurt Nayru. Veran summons monsters to fight Link. Link defeats the monsters and Ralph appears with the harp. Link stops Ralph from going to Nayru and accidentally teleports them both to a desert island.
The Pirate Captain
Link and Ralph make a raft to escape the island. A storm hits them while they are at sea, but luckily a ship comes by them. They climb aboard to find the crew are all skeletons. The captain asks them of news in the world, as he has had enough of reading books. Link asks if the captain knows a weakness of Veran. The captain asks Ralph to play some music on the harp. The song reminds the captain of when he was in love with a woman. He then orders his crew to set sail for Labrynna. Link reads the ships log to realize that they have been stuck in the storm forever. Link tells the captain that if he lets them go; he will be able to free the captain from the storm, so the captain can return to his lady. The captain agrees and gives Link a pendent with a picture of the captain’s lady, who is, in fact, Queen Ambi. Back at the tower, Raven halts the rebellion. One of Veran’s spies sees Raven talking with one of the workers, so she decides to look into his past.
Veran leaves Nayru’s body while she is asleep to dig up some information on Raven. Link plays the Harp and he and Ralph are transported back to Raven. Veran takes over Ralph so she can watch Raven up close. Raven, Link and Ralph(under Veran's control) return to the hidden village. Veran learns about the people hiding from working on the tower and that Raven is Link’s ancestor. Link tells the village that Veran can be stopped by Mystery Seeds, which Raven found on his travels. The villagers decide to attack Veran to free Labrynna. Veran destroys the mystery seeds and leaves Ralph’s body. Before she returns to Nayru, she summons Ramrock, a giant rock monster, to destroy the village. Link defeats the monster. Guards storm what’s left of the village. Raven agrees to leave the village with the guards, on the terms that the people will not be harmed. Link and Ralph save Raven before he is executed, and the Queen decides to stop building the tower because Cap'n still loves her. Enraged by the new turn of events, Veran leaves Nayru and possesses Ambi.
The Queen (Veran) orders the guards to stop Link, Raven and Ralph, who are saved by Nayru, who teleports them into the present. Nayru then teleports them back to the past, to where the villagers are hiding in a cave. Nayru takes Roperi’s flower and turns it into Mystery Tree using her harp. Ralph goes to stop Veran at the tower so the mystery seeds had time to grow. Link learns that Ralph is a direct descendant of Queen Ambi. Ralph threatens Veran saying that he would kill the Queen, stopping Veran, even if he has to sacrifice himself. The mystery seed is finally ready, Link takes a child’s Seed Shooter, and he and Raven hurry to the Tower. Link then shoots a Mystery Seed and exorcizes Veran from Queen, forcing her to assume her true form, a giant spider. Veran quickly traps Link in her web.
Veran's True Form
Link frees himself while Raven, Ralph and the Queen escape the tower. Link continues to battle Veran. Link finds some bombs and tries to blow up Veran. Veran climbs the walls of the inside of the tower to escape the blast. Veran spin webs everywhere, so Link runs to the roof. Raven re-enters the tower to help Link. Veran grabs Link and holds him in the air. Link cuts off some of her legs so she can’t move and then stabs her in one of her eyes. Veran traps Link again, but Raven saves him and together they kill Veran. Ralph runs in even though he is too late. Before the group can celebrate, the Twinrova sisters fly in. Now, with the flame of sorrow lit from Veran's death alongside the flame of destruction kindled from Onox's demise, they can finally summon Ganon, the King of Evil.
The Return of the King of Evil
Though Ganon is resurrected, only his strength could be summoned, not his intelligence. Ganon destroys the tower, but Link, Raven and Ralph are saved by the power of the Triforce. Link thinks that the tower crushed Ganon, until Ganon reappears under the rubble. On the horizon Link sees the villagers, guards, and slaves running to help them out. They fight Ganon until Link beheads him, destroying him instantly. The people celebrate that the poverty is over. Raven is knighted by the Queen. Raven thanks Link for this help and tells him that he is proud to have Link as his descendant. Nayru, Ralph and Link return to the present where everything is back to normal. Link returns to his grandparents where he sees the picture of Raven in the house with a bigger picture of himself from the past there too. Link continues to train with his grandfather before it's time for him to set out on a new journey.