The reason Derek knows that something is more wrong with Stiles than they know is the stillness. When he snarls or pushes at Stiles, he doesn't flinch, or flail. He just goes still. His breathing is even and his heart doesn't do that lurch that it used to which indicated his fear and panic even as Stiles was busy saying he wasn't scared. The problem now was that he really wasn't. Stiles had been jumped, terrified and beaten before. He hadn't stopped being scared. But now? Stiles had stopped being scared, and Derek had started.
When you think of Stiles and how he had jumped into the supernatural world with both hands, you certainly would have thought he was fearless. The truth about Stiles was that he was full of fears, but acted recklessly anyway. He's what people in war times would consider a hero. Someone who acts without thought of their own welfare, but only of those around them. Someone who fought their own fears to protect others less worthy.
So if that was the way Stiles acted when he was afraid, how would he act now that he was no longer scared. Derek really thought that the next time there was a fight (and god knew they were like in for one with the Alphas) that Stiles would not survive. He was Stile's alpha, he needed to protect him. He knew that Scott considered himself to be Stiles Alpha, but he wasn't anymore. When you submitted and gave yourself over to another Alpha, your pack went with you. Your pack became part of the larger pack. Even if you had your fingers crossed behind your back when you submit, it doesn't change that. Derek had know exactly what he was gaining when Scott submitted to him. He was gaining Stiles. That was worth any bullshit that Scott would put him through.
He knew that Stiles had cracked under the Gerard's hands and told him where they were. He didn't blame Stiles. He was human, and if wolves could be bent and made to tell secrets, what hope did a human have. But Derek didn't think that is was just that he had cracked and told on them that has Stiles unable to look him in the eye. It's more than that.
He wished that Stiles trusted him more. He knew that Stiles trusted Scott for the most part, so he had thought it would be better for Scott to find out what was going on. What was up with Stiles. But true to form, Scott picked the wrong time and the wrong place. Scott had broached the subject outside school. In the parking lot. While he got that Stiles was making excuses to avoid seeing them in private, Derek knew approaching Stiles about this in public was definitely a very bad idea. Apparently Stiles agreed with Derek's view point even while Scott hadn't. Derek was really beginning to think that Scott didn't know Stiles as well as he used too. It could be that Stiles had changed, or maybe it was Scott. Derek wasn't certain, but there was a different cadence or rhythm to their friendship. He's not the least bit surprised that Stiles blows off Scott's concerns. That Stiles tells Scott that he is fine, that there is nothing to worry about. He's not even that surprised that Stiles agrees to attend the next pack meeting. He knows that Stiles is just saying that to appease Scott and that Stiles will find an excuse to miss the meeting last minute. But the ruse works. Scott backs down and does shoulder nudges before backing down.
Derek waits until Stiles goes home before approaching him. It's quiet and he knows that the Sheriff is at work. He doesn't approach the way he normally would. He walks to the front door and rings the bell. Of course Stiles answers. He doesn't expect that werewolves know manners and that anyone other than humans would ring his door bell. Derek asks to come in. Uncertain Stiles lets him in. Derek asks for a cup of tea. Because tea is good and soothing, it gives Stiles something to do with his hands and it takes a while for the water to boil.
Stiles stays standing at the kitchen counter. He is facing Derek. Derek looks him in the eyes and doesn't let Stiles drop his gaze. "I am your Alpha. I will take care of you. I will keep you safer than I have been. I will notice when you are missing and will look for you. I will keep the hunters from your door. I know I have let you down. I know you have no faith in me. I hope you will let me earn it back. "
Stiles had dropped his eyes and started to stare at the floor when Derek had mentioned he would take care of him, but raised them again when Derek asked for a chance to earn his trust. "You all just left me there. Everyone was so concerned about Jackson and his being dead. No one cared what had happened to me. I expected that from most of you. I thought that you might come. If not for me then for Boyd and Erica. But you didn't and Scott didn't and it was just me. I survived. I got out alive and I don't want to talk about it."
Derek thought about what Stiles was saying and what he wasn't saying. "We will talk about it Stiles. Maybe not now, but we will. Because this has changed you and I'm worried about what those changes mean. For you, for the pack, for your Dad and for me." He notices Stiles suprise. "What, you think that no one has noticed?" He could tell by the way Stiles looks at him that he is surprised. "You are not scared anymore. Not of me, not of a lot of things. I want to know why that changed."
"What so that you can change it back! Well I'm not going back to being afraid. There are bigger and darker things out there in the night then the big bad wolf. Boohooo. Seriously that's what is upsetting you? I'm not scared of you anymore..." Stiles snort with derision.
"No. I would be okay if that was all it is...was. What is the bigger bad thing in the dark Stiles? I wish you would tell me. I know you're not ready yet, but I am here when you are. Or Scott..." He breaks off as Stiles shakes his head with a wry smile on his face. "Okay, not Scott. You can talk to me. I know what it's like to be so scared and angry that you just think it might be better if you were dead." Stiles looks at him then as if weighing his words.
"What do you want from me?" Stiles asks.
"A chance. A chance to earn your loyalty. A chance to prove I can be your Alpha before you walk away. I want your trust Stiles. I especially want to be able to be there to stop you from doing something that will leave your Dad alone wondering what he did so wrong to deserve his son dying too." He sees Stiles flinch slightly with the last sentence.
"So, you are offering to keep me safe? Even from myself? Is that it."
"Yes. Your instincts are off. You are feeling self destructive. I will protect you, even from yourself if I need to. Why are you hanging around the Argent girl?" He knows that others will see this as a leap in conversation, but it really isn't.
"Why? Scott loves her. You let her come to meetings. Why shouldn't I be her friend?" There is a bite to Stiles' tone.
"Because...she doesn't smell like she used to. Her scent is changed. I let her come to pack meetings because it's smart to keep your friends close..."
"And your enemies closer." Stiles interrupts finishing the saying. "I happen to agree. So what does she smell like now?"
"She smells like Kate." Derek bites out the name. Hating even now having to utter that word.
Stiles just nods like he understands. "I'm not surprised. But I think she is our best shot at getting Gerard." Stiles gets down the mugs from the cupboard along with two tea bags and fixes them each a cup of tea. "I'll give you your shot. But I want to work with you, not in the background. I want to be there when we find him. I want to give the final blows."
"I'll work with you. Meaning I won't leave you out of this. It sounds like you have her more fooled than she has either of us. So we'll work together. But Stiles..." He waits until Stiles is looking at him "I won't let you kill him. Beat him conquer him, sure. But the final blow will come from me." When Stiles looks angry and stubborn he continues "There is your Dad to consider. He's the Sherriff. It's one thing for me to kill, it's another for you. I know your mad/hurt/angry, but I want you to come back from that. Killing is something you can't come back from. I don't want you to know that feeling. You will need to trust me on this Stiles. This is one of those I'm protecting you from yourself things."
"We'll see." Is all Stiles says, but Derek knows he has made points that Stiles will consider. He may not have gotten as far a with Stiles as he would have liked, but they have at least taken two step forward. He knows they have made progress for certain when Stiles asks him to stay for dinner, so he agrees and stays.
When he leaves, he is certain that he has begun to make some in roads for Stiles staying with his pack. It makes him happy. He knows that he needs Stiles in his pack. Both his wolf and he agree on that. Stiles is important. That's the reason Derek stays in the neighbourhood. It's also the reason why he climbs into Stiles' room later that night and finds himself rubbing the young man's back as he sleeps, helping to keep the nightmares at bay. He is gone by morning, because Stiles never fully awakened and he didn't want to embarrass him.