Deaton doesn't appear in Season 2 until Scott shows up at the Animal Clinic one evening with wounds that won't heal from the fight he had with Derek in the skating rink. While there, Scott sees Bennett's body, torn up by the kanima and asks Deaton about it. Deaton explains that he's not sure what the creature is that killed Bennett, but the best place to find out would be in a book that the Argents have which would describe their past encounters with supernatural creatures.

While Scott is there, Chris, Gerard, and some redshirts come in to hear Deaton's analysis of the body. He tells them that the creature paralyzed its victim with venom through a slash in the back of the neck and then killed him by raking its claws up through his chest and lungs. He tells them that he doesn't know what killed him, but that they should all be afraid because this creature is very fast and very strong.

Once Scott and Derek figure out what and who the kanima is, they come to Deaton for help in stopping it. Derek wants to kill Jackson, while Scott wants to save him. Dr. Deaton only seems willing to help because of Scott's answer. He leads them back into an exam room and explains that he doesn't have anything that can stop the kanima's venom. Derek is open to other ideas. He tells him that he slashed its throat pretty deeply and Chris emptied a clip into it and it just got up again both times. Deaton asks if it's shown any weaknesses, and Derek tells him that it wouldn't go near water. Deaton asks if that's true of Jackson, and Scott tells him that Jackson is captain of the swim team. Deaton says that they're trying to catch two people: a puppet and a puppeteer. He holds a medallion up and then puts it on the table. They are also aware that the kanima killed Sean but the puppeteer killed Jessica. Deaton asks why the human had to kill the wife. Scott suggests that Jackson couldn't do it because his mom was killed while pregnant too, and was possibly murdered.

Isaac suggests that it could be part of the rules. The kanima kills murderers. If it killed Jessica, then the baby would die too. Scott asks if that means Mr. Lahey was a murderer. Isaac woudln't be surprised if that were the case. Deaton then suggests that the kanima's fear of water isn't from Jackson but from the master. "What if something that affects the kanima also affects its master?" He takes out a jar of mountain ash and pours a circle around the medallion. 

They formulate a plan to trap the kanima and its master. Deaton gives Scott a needle full of ketamine to knock Jackson out. It's the same thing they use on the dogs. Then he gives them some mountain ash and says this part is for Stiles and only him. Stiles is a bit put off by the amount of pressure. He has to make a line of mountain ash around the whole building and it will trap supernatural creatures inside. "Think of it like gunpowder. It's just powder until a spark ignites it. You need to be that spark, Stiles." "If you mean light myself on fire, I don't think I'm up for that," Stiles replies. Deaton smiles and tries again, explaining that the spark is a force of will. Deaton tells him that if it's going to work, he has to believe it.

After the attempt to capture the kanima fails, Derek brings Scott, nearly dead from wolfsbane, to the Animal Clinic. Dr. Deaton takes care of Scott while Derek watches. Derek looks a little ill from the wolfsbane, while Scott is completely unconscious. Derek thanks Deaton for his help, but Deaton doesn't reply. Instead he walks out to the front office to find Ms. Morell waiting. She tells him that she can't decide if she admires his sentimentality or despises it. He tells her that he doesn't want her opinion, but she gives it anyway. She thinks it's a mistake to let teenagers handle the troubles in Beacon Hills. He tells her that they're more capable that she thinks. She asks if he's going to tell them what's coming, but he think they have enough to deal with right now.

Deaton doesn't step in again until after Lydia has drugged Derek and used him to resurrect Peter. Lydia and Peter leave Derek on the floor of the Hale House, unconscious. Deaton calls him back with a dog whistle.  Derek smirks and tries to stand, but he stumbles. Deaton catches him and tells him that he's going to be weak for a few hours. Derek flashes back to Peter coming back to life and realizes it wasn't a dream. Deaton tells him that he's still an alpha, "but, as usual, not a particularly competent one." Derek lets the insult go and asks where Peter is. Deaton doesn't know. Derek demands to know why Deaton is helping him. "Helping your family actually used to be a pretty important part of my life. Helping you was a promise I made to your mother." Derek backs off and says that Laura told him there was a sort of advisor to their family.

Deaton says that Peter's resurrection comes with a price. He will be physically weak, so he will rely on his intelligence and cunning. "He's going to come at you, Derek. He'll try to twist his way inside your head, preying on your insecurities. He'll tell you he's the only way you can stop Gerard. Do not trust him." Derek replies that he doesn't trust anyone. Deaton replies that if he did he might be the alpha he likes to think he is. "Unfortunately, the one person you should trust doesn't trust you at all." "Scott." Deaton tells him to find Scott as fast as he can because Gerard always has a plan and it's so far going exactly how he wants. Derek spends most of the conversation looking worried, even while Deaton is insulting him. Having given his advice, Deaton goes back to Animal Clinic.

Scott still shows up for his job, despite all that is going on, and one night Isaac comes in while they're working on a dying dog. Deaton has Scott invite him back into the exam room. Isaac watches as they treat an injured dog. He asks why the dog smells the way it does. Deaton smirks. Scott said something similar to him awhile ago. All of a sudden he could tell which animals were getting better and which weren't. Isaac looks like he's about to cry when he says that the dog isn't getting better. "Is it cancer?" "Osteosarcoma. It has a very distinct scent, doesn't it?" Scott nods in agreement. Deaton invites Isaac to come closer. He says that Isaac knows what his abilities can do for himself, but he'd like him to learn what they can do for others. He asks Isaac for his hand, and then places it on the dog. 

Without really meaning to, Isaac starts drawing the pain into himself. He pulls back his sleeve to watch the black threads move up his skin. "What did I do?" Isaac asks. Scott tells him that he took some of his pain away. Deaton explains that it was only a little bit, but sometimes even a little can make a big difference. Isaac starts to cry, and Scott tells him that he cried the first time he did it too.

When Scott has his final showdown with Gerard, he reveals that he had developed a plan awhile ago with Deaton's help. There are flashbacks of the two of them making pills fille with mountain ash. Scott is shown switching Gerard's pill box for one filled with the faked pills. This switch prevents Gerard from successfully getting the Bite from Derek and ruining his plan.