So for anyone who comes here from my author page, yes this is different from my normal style but I have been playing around with this idea for about 3 months so I am happy it's finally out of my brain and into the internet

Warning: kidnapping and mention of torture

This takes place between episode 7 of season 3 (the one in which Deaton gets kidnapped and Scott finds out he's a true alfa) and episode 10 of season 3 (in which they're trapped in the hospital and Scott gets revealed to the others as a true alfa)

So… Only Deaton, Scott and the Alfa pack know of him being a true alfa.

It had been a week since Scott had disappeared, no death threats, no sign, and no nothing. Even with 2 werewolves on the case, they still could not find a sign of Scott. A week and still, nor Isaac or Derek could get his smell. They had no link whatsoever to him.

So when they heard a howl, a howl that sounded suspiciously like Scott's, during a lacrosse game, they went after it. Anyway, because of how close it sounded, the game was stopped. Alison, Stiles, Isaac and Derek (he wanted to be out looking for Scott but also needed to protect Isaac so he was at the game) ran into the woods and pretty quickly found a warehouse that had mountain ash surrounding it, confirming that someone was trying to keep supernatural creatures out, or In. Stiles destroyed the barrier and they ran in.

They found Scott tied up (think when Derek was taken in season 1) with electric charges going into his body, they saw multiple gashes on his torso, most looked as though the person keeping him there was poisoning him with wolfsbane. They also saw a man in the corner with a remote, happy with the wolf's screams of pain. Alison was the first to react and kicked the remote away from the man. She then restrained him, but while doing that she noticed who it was. Gerard Argent.

The other's went over to Scott and cut him down. Derek looked him over and asked Stiles to go get whatever kind of wolfsbane he could find. Stiles chose to not make a snarky comment at that.

"Hey Scott, you with us," Derek asked trying to gauge how much damage Gerard had done

"mhmh mhmh" Was Scott's response, still spasing a little from the electricity.

They then heard what sounded like multiple gasps, and a whine of pain from Scott. Both werewolves turned, realizing that multiple citizens had come in without their knowledge. Then Stiles came back into the room

"Hey, I found it." Stiles cried out ignoring all the random citizens. Scott whine once again in pain

"Hey, anyone got a lighter" Derek asked the citizens. One of them, who happened to be the coach, took it out and Derek grabbed it and turned back to Scott and Stiles. Stiles was hovering over Scott "Stiles, give it" Derek asked. Stiles gave it to him "Scotty, you ready" Derek asked Scott, knowing it was going to hurt

"D…Do… I…It" Scott stuttered

"Stiles, Isaac, hold him down," He said starting to poor the wolfsbane on the affected areas

He then lit the lighter and put it against Scott's skin. Scott tensed but kept himself from shifting and from making his eyes glow. After a minute it was done, with most of the residents from beacon hills having or left to call 911 or turned away. After it was done Allison came back from tying up her grandfather, bringing him with her. Scott was breathing somewhat normally and they thought it was over until…

Scott's head turned quickly to look at a corner. His eyes were flashing… orange? Before anyone could say anything, Scott was on his feet staring at the corner. The other werewolves were on their feet too but couldn't sense anything. And yet Deucalion stepped out of the shadows

"Why, what do we have here," Deucalion said smirking

Scott had to stop himself from attacking him immediately. Ethan and Aiden, who were in the crowd of people earlier and had left it to the hands of Derek, had come back in when they heard Scott get up. When they entered they saw the tense eye contact between Scott and Deucalion and even though they had no idea what was going on, they had a feeling Scott had a reason.

Without even waiting, Deucalion jumped on Scott, forcing him to the floor were both rolled around for multiple seconds. Derek and Isaac were jumped by other pack members (not Aiden or Ethan) and they also started fighting. A minute passed, both Allison and Stiles were trying to be useful as Aiden and Ethan just waited. After another minute, Scott was thrown into a wall by Deucalion. Everyone turned at the sound of him hitting the wall, but what they saw was different. They saw Scott, standing straight, looking directly into Deucalion's eyes and the weirdest part, Scott's eyes were Red, as in alpha red. Everyone was looking at him, but Scott didn't seem to see them, he was too occupied giving Deucalion a death glare, and before anyone could do anything, Scott jumped at Deucalion. After another minute of fighting, Scott blocked a punch that was made for his stomach, but then Deucalion threw something into Scott's face, something that burned, mostly his lungs. He backed away from Deucalion as he started coughing, trying to get the unknown entity out of his lungs.

Deucalion and the rest of his goons left, leaving only: Scott, who was now on the floor coughing, Derek, Isaac, Stiles, Allison, Gerard, who was still handcuffed, Ethan and Aiden. Everyone, but Gerard, came close to him, but the werewolf's immediately backed away

"What?" Allison asked

"He has wolfsbane in his lungs, what Deucalion threw in his face was probably that" Derek explained

"No, No way did Deucalion use Wolf's bane. He hates that stuff. He would never throw that in another Alphas face" Ethan practically yelled. The others all looked at him weird

"Well, Scott isn't an Alpha, so are you sure he wouldn't" Derek Yelled back. Scott whined and this caused, even more, coughing from the young Alpha

"This isn't the time for this" Allison said, then turned to Gerard "What can we do to help him," she asked

"Nothing," Gerard said laughing, "Gassed wolves die in minutes, hours maybe" Gerard continued

"Get him out of the warehouse," Derek said, grabbing Scott by the arm. Isaac, understanding what he wanted to do, grabbed Scott's other arm and brought him outside.

Scott was leaning on a tree stump, taking deep, shallow breaths. Everyone was scared for him, but compared to the others, Allison did something. She took Gerard to the police, explaining what she had seen and that the others that had seen it was with Scott, trying to get him to calm down. She then went to her father and told him the real story. Chris then went to his car and grabbed a syringe and told Allison to get them back to the group.

After what felt like hours, but was probably just minutes, Allison and Chris got back to Scott. Scott looked even worse, he had black veins on his face and was breathing shallowly. Chris came down so that he was looking into Scott's eyes before plunging the syringe into his chest. Scott didn't even have the energy to scream. His body jerked before he went unconscious. Scott seemed to relax after a second and the veins on his face retreated. His breathing became more regular and the others finally let the breath they hadn't noticed they had been keeping.

"He should hopefully be fine," Chris said after checking Scott's pulse

After a minute, Scott started to wake up but he kept his eyes closed and just seemed to be listening to the wind. After another couple of minutes, he opened his eyes. Isaac, who was the first to see him, told the others "Hey, Scott's awake" Which caused Scott to close his eyes and put his hands to his ears

"Don't yell" he heard Ethan say. He knew that Isaac made a face at that

"Hey Scott, you okay" He heard Derek's voice. He carefully opened his eyes to see the older Alpha staring down at him. Scott nodded his head and replaced himself to a more comfortable position leaning on the tree.

"Where's Gerard" Scott asked after a second

"Allison brought him over to the police" Came Aiden's response. Scott nodded his head before closing his eyes once again to listen to the wind and to try and block out the dull pain in his head. Chris had gone over to the parking lot to try and intercept Deaton, who he had called after Scott went unconscious

"You okay" he heard Derek ask

"a Headache" Scott responded. Scott didn't see but the twins looked at each other in recognition

"Scott, can you show us your eyes," Aiden said, knowing it sounded weird

"Why?" Scott asked

"We want to check something" Ethan answered. Scott not knowing what they were talking about opened his eyes

"Your werewolf eyes" Aiden clarified. Scott did as he was asked and turned his eyes to what he thought was yellow. Derek saw the red and was incredibly confused, same with Isaac and Stiles

"Why are your eyes red?"

"What," Scott said as his eyes turned back to normal

"You didn't tell them," Aiden asked as he looked between Scott and Derek

"Tell us what?" Derek asked

"Scott's an alpha now," Ethan said

"But, no one's dead and his eyes were yellow earlier," Isaac said

"They were orange, not yellow" Aiden explained. Scott had closed his eyes again and had put his hands to his ears again

"What the hell does orange represent," Stiles asked

"It represents the shift between alpha and beta or in Scott's case omega" (I feel like Scott is an omega that is allied with Derek's pack) Aiden explained

"He's a true Alpha isn't he," Derek asked

"Yes" both responded at once

"What the hell is a true alpha," Stiles asked

"It's an alpha that doesn't need to steal his powers from another and can rise up by his own strength of will" Deaton answered having appeared at some point

"So what, Scott's now an Alpha is what you're telling me and that he didn't have to kill anyone for it," Stiles said

"Yes" Deaton responded

"Okaayy" Stiles said

Deaton bent over to Scott who still had his hands to his ears. Deaton carefully put his arm on Scott so that he would look at him and then gave him a sign to lower his hands from his ears. He did so carefully. After a minute Deaton talked

"Are you okay Scott?" Deaton asked keeping his voice down. He got his response when Scott flinched at the sound "Scott can you try to get your hearing under control" Deaton asked even lower and let Scott focus for a couple seconds before said boy nodded. "You sure," Deaton said a lot louder and was happy to see Scott not flinch

"Yeah," Scott said

"You ready to go talk to the police," Deaton asked

"Well it depends, how are we explaining the fact my cuts are healed and that Derek burned me with something"

"I can take care of it," Deaton said and then let Scott, with the rest of his friends walk back to the School. Looks like Deaton's emissary days weren't over.