Though the Hyrule Historia has revealed the official timeline of the game, I've created a "fictional" timeline specifically for this story, as you'll see below, that shows how the past events have led up to the moments in the story.

Any kind of critiques and comments would be GREATLY appreciated.

Minish Cap→ Four Sword → Ocarina of Time →Majora's Mask → Four Sword Adventure → A Link to the Past →Twilight Princess

"...I'm coming for...YOU!"

A dark figure with red eyes with a peculiar sword lunges forward and Link wakes up with a yelp, his face drenched in sweat. Link finds himself in his tree house in Ordon Village, he looks around but no one is in the house besides him. Soon he hears his friend Fado call his name form outsides. Beckoning Link to the ranch to help herd his Ordon Goats with the help of Epona. Link mounts Epona and rides into the Ordon Ranch and begins to herd the sheep. Soon Link begins to develop a slight headache. Nausea starts to develop and Link eventually loses his motor skills and an Ordon Goat accidentally crashes to him knocking him off Epona and falls unconscious. He later wakes up in Rusl and Uli's house with Colin moistening his forehead with a warm and wet cloth. Fado is also there apologizing for what happened. Link shows him that it wasn't his fault. Colin and Rusl both ask what happened but Link doesn't know.

That night, as Link was half asleep, he hears a loud scream. He runs out of his house and into the village into a massive rainstorm and discovers that the Mayor's house has been struck by lightning and has caught on fire. Without thinking, Link immediately rushes inside and finds Illa and her leg caught under a burning branch. Link lunges at Illa and removes the branch, picks up Illa in his arms and sprints out of the house right before it collapses. Outside Illa is relieved to see that her father has made out fine, being saved by Rusl and Colin. Mayor asks Link if he will take Illa to the Ordon Spring to heal her leg. Link, still hold Illa in his arms walks to Ordon Spring. Link sets her down in the water of the spring and washes her leg in the mystical water. Illa beings to thank him "When I was in that burning house, that last thing that thought was whether I would be able to see your face again, Link ", Illa says as her eyes fills with tear.
Link creates a smile as his eyes tear up as well. Both Illa and Link move closer to each, appearing to about to have their first kiss... when suddenly...

Black lighting descends upon on the spring, the Great Fairy appears screaming in great pain and agony then she disappears. A dark spiraling vortex takes form in the sky and ominous wind blows through the area blowing Illa, the Ordon villagers away into the night sky and destroys the rest of Ordon Province. Then, Ordona appears lying over in the spring wounded "Link...Hero..."

That's all that leaves Ordona's mouth before a blinding light flashes. Link finds himself in a gray atmosphere and hears a familiar voice calling to Link from the Twilight Realm; asking for his help.

"Link!...Link!...Please!...Help!...Help! Us! Its Midna!"

"If you don't do something, the 2 worlds will combine! Help! Please!"

"Ordon...was the last!"

Link tries to reach out, but then finds himself back in what used to be the Spirit Spring, but dried up. The trees were nothing but barren branches and all of the fairies of the spring are on the ground, dead. Link then realizes he's back in his Hero's Clothes and has his Hero's Shield. Link races to Hyrule Caste Town, to find it on fire. He ventures into the castle to find the now Queen Zelda with a despaired expression on her face. "Link...the Great Fairies of the Springs...they're gone!

The same ominous wind blows through the city but with more destructive force than in Ordona, destroying the tower but Link catches Zelda giving her one last chance to give one final message before she is finally blown away. "Please..! You must get to the Arbiter's Ground…! Find the new Queen of the Twilight Realm!"

That's the last thing Link hears, before she is blown away.

Before he does, Link immediately heads to Kakariko Village. The village is destroyed, all of the houses are demolished and the Spirit Spring is in the same condition as the Spirit Spring in Ordona. Link fortunately finds all of the inhabitants of Kakariko and all the Gorons with a few Zoras in the shelter under Renaldo's sanctuary.

"Brother! You're Alright!

Says Darbus

"Thank the goddesses you're alright."

Renaldo expresses with a sigh of relief.

"There is a plague spreading all over Hyrule!"

"Yes, I believe so."

Says one of the Goron Elders.

"Link, a few days ago I saw a dark, ghostly standing in front of the Spirit Spring that looked just like you with a black bow and arrow. The figure fired a black arrow at the Great Fairy in the spring. When the arrow hit the spring, the fairy was destroyed. I thought it was you, Link but then I realized that it would never be you as you are the descendant of the Hero of Legend plus, when the Great Fairy was destroyed the dark figure disappeared."

They all gasp but they all know that Link would never do something as evil as that.

"What...What about Lanayru Province? The Zora's Domain? Renaldo asks.

"I'm afraid that the same thing has happened to that Province."

The Elder says

"Brother...Please go find what happened to the Zora's Domain."