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.
Meanwhile in Hyrle
Zelda has just finished translating the notes left by The Hero of Time and has just found a series of notes for a song, with a note underneath saying that this song can only work in Termina, while the other song (The Song of Time) could work in both realms, but they both have different effects based on which realm it was in.
"Alright, I wonder if Midna has anybody in Termina that could use this song in Termina to help clear the barrier" Zelda wondered to herself. She then copied down the song notes and started heading out towards Link's hometown.
Around the same time in the Twilight Realm:
The realm portal gun has been placed in a side-room to the castle. One of Midna's few remaining guards has finally managed to reach the Shadowy Castle. He is currently masked and wearing a large robe, completely hiding his body. He enters the castle, and sneaks around the castle, eventually sneaking past the guards and finding the gun. He powers it up, and opens the portal, however when he arrived through the portal, he realised he wasn't in the realm he thought it was in.
"I need to find Minda, she's hurt, I saw her slip on the ground in Hyrle" the figure said. He then looked around, and saw a nearby large wall.
"Maybe there I can find out where I am" the figure said as he started walking towards the town.
Back to the Poisonous Temple
Link and Midna have just arrived at the first room of the Poison Temple and almost immediately, four Poison Vipers jumped out of the large pool of poisonous liquid sitting in the middle of the room and lunged at them. Link immediately blocked the two Poison Vipers that lunged at him with his Shield, while Midna stopped the other two in mid-air. Midna then flung the two across the room, taking them down, while Link slammed the two Vipers into the ground, then stabbing them one after another with his Sword. Two chests then fell down.
"What are these?" Midna asked curiously. Link replied with "They must be chests. I wonder what's inside". Link opened the first chest, and discovered a Dungeon Map. Midna opened the second chest, and discovered two small keys. Link started looking around, and soon found a couple of doors. He turned to Midna, and said "Can you please pass me a Small Key?" Midna nodded, floated over, and have the key to Link. They both opened the doors, went through it, then temporarily returned to the first room.
"Hey Link, this puzzle looks like it needs 2 people to solve" Midna said. Link nodded, then said "I think I have an idea. The item that is blocking our way is moved, how I'm not sure, then you go through and press the next button. That does something, we'll just have to wing it for now". Midna nodded, and they passed back through the doors.
Link found a switch. When he pressed it, he noticed that nothing had happened. Midna, however, had a row of Spikes disappear from in front of her. She went through to the next section and pressed a button, opening a door for Link. When Link saw this, he realised that the buttons were alternating between him and Midna, and that there must be a set of switches on Midna's side opening his walkways. So Link and Midna pressed the buttons to allow the other to go through, and eventually got to the end of their corridors, where both Link and Midna got a Small Key to go through the door into the next room, where they reunited.
They then turned around and saw a Purple-coloured Armoured Axe-Wielder standing before them. Link recognised it immediately, it was a Poison version of the Darknuts he had encountered six months previously. Link was also familiar with how hard they were to defeat. The Darknut then rose up and started charging at them, forcing them to split. Link raced around the behind the Darknut, but it turned around too quickly, forcing Link to leap to one side to avoid the swing of its huge axe. Midna, seeing Link struggling against the Darknut, use her telepathy to freeze it in place. It was about then that Midna realised that the Darknut was also resistant to magic, as it turned around and the shield bashed into Midna, knocking her to the ground and dealing almost a third of her maximum heart counter in damage. Link, seeing an opportunity with the Darknut turned away from him, swung as hard as he could with his sword, dealing a moderate amount of damage, but forcing Link to put his shield up to block the axe, leaving a large dent in the shield. Midna recovered, firing off an electrical-like blast from her fingers to distract the Darknut, but the Darknut was ready. It immediately turned around, forcing Midna to duck. The Darknut then swung back, preventing Link from getting a major hit on it.
"What do we do? This is nothing like the Darknut's I've encountered before" Link said, dodging another swing from the large axe. Midna fired off another electricity-like attack, dealing heavy damage to the Darknut and breaking most of its Armour. Link, remembering what will happen when all of its armour is gone, said "Midna, this Darknut will get very agile once the remainder of its armour is gone, so be careful". Midna nodded, and leapt upwards using her telepathic abilities, using one final pulse to break the last of the armour.
The Darknut then violently swung its sword around, narrowly missing both Link and Midna. Midna continued to fire shots from behind, while Link managed to get a couple of hits on the Darknut between dodging all of its attacks and having to block the huge sword with his shield. Once the Darknut finally fell, Midna returned to just above the ground and said "Wow. Tough foe". Link nodded, then saw that the two sets of stairs now were able to be climbed, one down and one up. Midna, thinking for a moment, wondered "Well, which one is the right one for you and me?" Link replied with "I get the feeling that I should go up the stairs, and I need my wolf form to complete it" Midna nodded, and Link climbed the stairs, where immediately he realised that he wouldn't be able to complete it without heavily damaging himself. Returning to the first floor, he said to Midna "Alright Midna, I'll have to run the lower floor, the floating spikes on the upper floor would heavily hurt me" Midna nodded, then said "I'll go up the stairs, while you go down. We need to open the door, but it looks like it has two switches" Link nodded, and descended the stairs, while Midna ascended.
We will firstly follow Link then we will follow Midna.
When Link descended the stairs and saw his obstacles to get to the other side, he quickly realised that he would need to go into his Wolf form to pass through. Transforming into a Wolf, he leapt the large gap between the two platforms, immediately leaping into a bite on one of the Vipers that were about to attack him. Picking up the Viper in his mouth, he threw it at the other one, killing both of them.
He transformed back into a human, and started looking around. After a few moments, he realised that there was a pillar of wood, where he could use his Hookshot to get up. Firing his hookshot, he arrived on the third platform. At this he was ambushed by a Twilight Bloat, which he didn't even see coming. He returned to his Wolf Form and activated his sense ability, which is realised he had never done without Midna. It still worked though, so he activated it. He saw it electrify, and leapt out of the way to avoid it. After a few minutes of mauling the creature, the Twili Bloat was down, leading to a large chest falling away from Link. He turned back into a human, said "I'll be honest, I don't like being in my wolf form" then headed towards the chest.
When he arrived at the chest, he opened it and revealed a pair of gloves. But they weren't any old gloves, when Link put them on, he felt a tingling sensation, followed by a small voice in his head that said that he would now take no damage from Poison.
"Cool" Link said. He then activated the switch, then headed back.
Meanwhile with Midna
Midna arrived on the top floor and soon realised why Link didn't want to go across this part of the temple. She knew that she could float across to the next platform, and fired off a telepathic pulse at the viper trying to fire off poisonous spit at her, destroying it before it could fire off another shot.
"Alright, so where do I go?" Midna asked herself, looking around the area. She saw something rise up from the ground, and she immediately fired off several pulses to damage it. The Poisonous Giant Viper leapt at her, but she avoided it easily, continuing to fire off pulses until the Giant Poison Viper was down. Midna floated over to the switch on the other side of the top floor, and activated the switch. In addition to opening the other lock, another treasure chest fell down. Midna opened it, and found a purple cloak. Since she didn't have the chance to grab her cloak when she fled the Twilight Realm, she threw it around herself, and a small voice in her head said "You now cannot be Poisoned" Midna nodded, then headed back towards the first floor.
Link and Midna reunited on the first floor, and saw the door open to the next room. Midna turned to Link and said "So, if that Darknut was that hard, How are we going to defeat Vexona?" Link replied with "I don't know honestly, if the Darknut was just the mini-boss, then Vexona's going to be even harder". Link and Midna then went through the door and into a hallway. Where several Poison Vipers were waiting for them. They attacked Link and Midna with the Poison shots, but despite doing a heart of damage to both of them, neither of them were Poisoned. Link then sliced the Viper in half, while Midna used telepathic pulses to destroy the other two.
Another two treasure chests fell, and when Link opened the first one, he found six hearts, which he gave to Midna, as she had lost seven of her fifteen hearts while Link had only lost three of his twenty-five hearts. Midna opened the other one and found a Small ley, which she used to open the door to the second-to-final room. Here, they found another two giant Poison Vipers.
"Here we go" Midna said. Link nodded, and when the two giant Poison Vipers struck at them, Midna avoided it while Link stopped it with his Shield, before stabbing into it repeatedly until that Giant Poison Viper died. Midna took a few shots, but she had to avoid the tail swinging at her. Link, seeing that the tail was going to stab Midna, he blocked it. He didn't have enough time to put his shield up, she he just swung his sword, but it still struck his arm. Link doubled over in pain, feeling the edge of the tail sliced the side of his arm. Midna fired off one final telepathic pulse, and killed the second giant Poison Viper.
"Are you alright Link" Midna said as Link pulled himself up. Link checked his heart counter, and found the Tail Stab had stripped him of a huge ten hearts. Shocked, Link asked "Do you have any healing abilities?" Midna shook her head. Link then took out a small knife, and sliced the sleeve of his shirt off, then used it to bandage his injured arm.
"Nice" Midna said. Link nodded, then opened the large Treasure chest. Inside, was a boss key.
"That'll be to open the room that Vexona's in" Midna said. Link also found a heart container, which he gave to Midna, but she broke it in half, and gave half of it to Link. The hearts of both Link and Midna were both fully refilled. They then walked towards a huge door, with a keyhole that looked perfect for a Boss Key. Midna put the key in the door, and they went through to face Vexona.
A/N: Wow that was long. I think I'll use the next chapter to do the battle between Link, Midna and Vexona. Stay tuned to chapter 6, VS Vexona.