Throughout Season 1, Dr. Deaton is largely just Scott's boss. Sheriff Stilinski regularly comes to visit him to ask for his professional opinion on the animal attacks that have been happening around town, but Deaton either lies or evades his questions. He claims to not be an expert and lets the Sheriff come to his own conclusions.
Based on a flyer with a deer with a revenge spiral on it, Peter and Nurse Jennifer briefly convince Derek that Deaton is the alpha. Derek attacks him in the clinic and roughs him up, but Scott stops him before he can do any permanent harm. Scott convinces Derek to meet him at the school, where he intends to summon the real alpha.† Derek packs Deaton into the back of his car and brings him to the high school, but he escapes while their backs are turned. His disappearance coincides with the appearance of the alpha, and Scott and Stiles start to believe that he must be the alpha as well.†
After Scott is shot by Kate and her hunters, he passes out in the woods. Deaton finds him and brings him back to the clinic to remove the bullet and help him heal. Scott is confused, and Deaton tells him that 90% of the time he just deals with cats and dogs, making clear by implication that the rest of the time he deals with stranger sorts of beasts.
Scott passes out for a while, and when he wakes up on the exam table, he immediately hops up to try to leave. Deaton suggests that he stay, but Scott can hear Peter come in the front of the clinic. Deaton insists that Scott stay and goes out to take care of Peter. He's calm and states that the clinic is closed when Peter tells him that he's come to pick something up. Deaton is fearless in the face of Peter's rage, confident that he won't be able to get in and take Scott. When Peter tries to rush at him, he's stopped by the small gate of mountain ash wood that divides the waiting area from the back of the clinic. Peter sneers and gives up.†