Disclaimer: With the exception of the characters found within the temples (Although some are based on Legend of Zelda villains), Legend of Zelda is owned by Nintendo.
Chapter 1: Flight of the Twilight Princess
It was a typical day in the Twilight Realm. While the Twili are going about their day, hundreds of miles away, a large, dark castle is standing in the darkness. In the deepest, darkest depths of said castle, a mysterious figure is floating, suspended in Amniotic fluid. A large, reptilian creature with enormous fangs slowly walked up to the figure, and said "My lord, my viper troops are ready"
The creature in the fluid replied with "Good, now, do you know where the castle of the Twilight Princes is?" to which the reptilian shook his head. The creature in the fluid replied with "I didn't think so. It is really easy to get to the castle. The only problems I can see with your troops is the distance"
"Elaborate my lord" the reptilian creature said. The creature in the fluid then said "Alright. The distance from here to the castle the Twilight Princess resides in is almost six hundred and fifty kilometres" the reptilian then asked "Should I capture the Twilight Princess alive?" the creature in the fluid replied with "Alive? Alive?, we shouldn't capture her alive, we MUST capture her alive! She is paramount to our plans, both in the Twilight Realm and in the Realm of Light"
"Alright, I thought so, I better get going to prepare my troops" the reptilian said and the Dark Figure nodded. The reptilian then departed.
"Lieutenant Viper Razor returns" one of the troops called as the reptilian creature returns to them. "Alright my armoured vipers, I hope our weeks of extremely long range training will pay off, because we are heading for the castle of the Twilight Princess" Viper Razor said and the troops cheered.
"It's great that our lord has picked our infantry to take the Twilight Princess, but we need to focus" Viper Razor said authoritatively and the troops called to arms.
"Now while her troops may stand no chance against you, the Twilight Princess is still very powerful. We must also NOT!... KILL!... HER!..." Viper Razor said, putting an extreme amount of emphasis on the last three words. One particularly large troop member then stepped forward.
"How do we capture her without killing her?" he asked. Viper Razor replied with "One of my powers allows me to trap anybody in a chaos net. She will break out of it at full strength but once she is weakened I can capture her". The troop member nodded, then stepped back. "Now let's go!" Viper Razor said and the troop headed out of the castle, heading for the castle, several hundred kilometers away.
Meanwhile in the Palace of Twilight, the twilight princess, Midna, was watching the twili as they went about their day through a window at the top of the castle. It had been six months since the events of Legend of Zelda: Twilight Princess and Midna was longing to see Link again.
"My lady" came a voice from behind Midna, and she pulled herself away from the window to face her.
"What were you doing?" the maid asked. Midna replied with "Just looking out at my constituents, and at the twilight". The maid nodded, then asked "You're still longing to see that Light Realm boy, aren't you?" Midna blushed, and asked "How did you know?". The maid replied with "Oh I recognise when someone is longing to see someone they haven't seen in a while, having experienced this a few times myself" Midna smiled, mainly because this was true. "Why are you here?" Midna asked, turning back to look outside the window.
"Some people are starting to worry about you, with all the time you have been spending in your room, they thought that you may be sick or something" the maid said. Midna turned to face the maid, and said "Alright. I''ll go down to address them, I'm sorry I worried you" Midna then walked past the maid and headed down the stairs.
When Midna got to the bottom of the stairs, she saw several of her guard and maids. "There you are Midna we were getting worried about you" one of the maids said. "Sorry I worried you, I've found it best to observe the constituents from my room, and I've been longing to see my Light realm friend again" Midna replied. Just then, a guard burst into the room, panting.
"The southern guard has, just been obliterated by, some weird vipers, they're heading, this way" he said. Several guards turned to Midna, and one of them said "We have to get you to the north castle, you'll be safe there" but the panting guard said "She won't be safe no matter where we go. These vipers are far more powerful than anything we have ever seen, it's Midna they're after" Midna nodded, then said "Get the cannon ready, if it works, I can escape to the Realm of Light. The crest I am wearing means I can still go into my Imp form, and I can escape from these beasts"
"What will you do if you get into the Realm of Light?" The panting guard asked.
"That boy I always talk about? I'll find him, and we will work together to find a way back here to destroy these foul creatures" Midna replied. Signalling to the other guards, the panting guard ran out to confront the vipers. One of these guards got to the cannon, and started charging it. Midna meanwhile ran towards the edge of the landmass, yelling to her constituents to get inside. As the vipers appeared, they all charged for Midna, completely taking down the guards within seconds. The remaining guard fired the cannon, just as a viper struck him with its barbed tail.
Midna jumped through the portal, but the moment she landed on the ground, her left ankle flicked to one side, then the other. Midna fell, and smacked her face into the ground, the crest falling to cover her face. With several viper's making it through the portal, but Viper Razor not, the vipers that made it through had no idea what they were doing without their leader. After a few moments of not being able to find Midna, they left.
After more than a minute, Midna, now in her Imp form, floated out of her cloak, and holding her injured ankle. "My ankle's wrecked, I need someone to fix it. I can't do it on my own" Midna said, wincing at the pain of her ankle. She looked around, and recognised that she was in Hyrle field. Continuing to look around, she eventually found a castle. "That must be Hyrle castle" Midna said, floating towards the castle.
A couple of hours later, Link was walking through Central Square, and just as he passed West road he saw a strange shadow moving about it. "Huh?" Link said, looking more intently at the road. Link reached the edge of West road, and said "Who's there?" but after a few moments, all that Link saw was a dog run out of a nearby alleyway. "Oh, it was just a dog" Link said, kneeling down and patting it. "Alright, run along now" Link said and the dog ran past him. Link then headed for the field, where he could train with his sword and bow.
Midna meanwhile was watching Link from a nearby alleyway.
"I'm not sure Link saw me, but I hope he comes looking for me" she said, watching Link walk away from her. She heard a new set of footsteps from the right, she flew back into the shadows so nobody could see her. A soldier walked past the alleyway that Midna was in, and briefly stopped, looking down the alleyway. But he merely shook it off and kept walking. "I hope he didn't see me" Midna said, watching him walk away.
After Link finished his training, he walked back towards the castle. Again, he walked past the West road and again, he saw the strange shadow he had seen before. "Someone's there" Link said. There was no denying it this time, someone was there. Link was searching down the West road when somebody said "Link, what are you doing down there?" Link turned around and saw a guard addressing him. "I thought I saw someone familiar" Link said. "Well you had better get out of there, that place is dangerous" the guard said, and Link, nodding, left.
That night, Link was watching outside the castle, overlooking the market. "Everything OK Link?" Zelda asked. Link replied with "I thought I saw Midna today". Zelda looked at him, looking puzzled.
"Are you sure you saw Midna?" Zelda asked and Link replied with "I'm not sure, but who else do we know has a form that looks like an Imp? Other than Midna" Zelda thought about this for a moment, then said "If it truly was Midna, why didn't she come out for you?". Link had his reply almost instantly. "She doesn't like the light of our realm. I only briefly saw someone that looked incredibly similar to her Imp form" Zelda then put her hand on Link's shoulder and said "Then we'll look for her, let's get going" Link nodded, and they both headed out towards the market.
Link showed the guards pictures of Midna in her human form and her Imp form, and said "If she shows up in front of you in either of these forms, call us" they then proceeded into the market.
Link and Zelda started by showing Midna's photos to every guard in order to put them on watch for Midna. They then proceeded out into the Central Square.
"So where did you see Midna?" Zelda asked. Link responded with "In there, in the West road, I saw her in the alleyways" so they split up, and searched each of the alleyways without success. Link however, encountered a Chaos Viper who instantly fired it's tail at Link, who only managed to avoid damage by putting up his shield. Link then struck the Viper, and fired it back. Link charged at the Viper, and struck it several times, eventually destroying it. "Whoa! What was that?" Link said. Just then, another Viper came up and struck him. "ARGH!" Link said and Zelda came running for him, firing the Viper off of Link.
"Are you OK?" Zelda asked. "Yeah, that Viper bit me, but I'll be OK" Link replied. The Viper lunged at them, but a huge hand came out of the shadows, catching the Viper and throwing it into the darkness.
"What the?" Zelda said, surprised. Link however, charged into the shadows, for he recognied that attack, only Midna had hair that could do that. When he got to the other side of the alleyway, however, all that was left was the Viper evaporating. "Midna!" Link yelled.
Midna however didn't come out, because she was now overwhelmed by the pain of her ankle, she was struggling to stay awake. But because she was so tired, she couldn't cry out in pain, despite the fact that, by doing that, Link would almost certainly find her. But she couldn't muster the energy.
"Link" Zelda yelled and when Link turned around he saw Zelda running up to him.
"Are you OK?" Zelda asked. Link replied with "Yes". Link then added "But Midna isn't. She's hurt, or sick or something, something'swrong with her, and I want to help her" Zelda then looked at Link and said "Let's go back home, we can go looking for her tomorrow" Link however, was still very worried.
"I'll be out to look for Midna at first light" Link said, but let Zelda pull him back to the castle.
Meanwhile back at the castle of darkness, Razor Viper returned to address the creature in the fluid.
"My lord, I'm sorry, but I did not expect the Twilight guard to have a cannon to let Midna escape into the Realm of Light. Some of the troops got into the Realm of Light but I have lost all contact with them"
The creature in the fluid replied with "That is dissapointing. How many did you lose in the exterminations?"
"Outside of the half-dozen that wound up in the Realm of Light, two" Razor Viper said.
"Well you still have the vast majority of your team, and we can get our other factions to gain control of the dungeons" the creature in the fluid said. The creature in the fluid then concluded with "Now be on your way" and with that, Razor Viper departed.