Rafael McCall is Scott's father. He works for the FBI. Scott lived with him for a while after he and Melissa divorced, although she appears to have full custody now.
Agent McCall is in town to acquire evidence in an impeachment case against Sheriff Noah Stilinski. He didn't tell either Melissa or Scott that he was coming to town, and neither are happy to see him.
After Scott learns about the impeachment proceedings, he calls his dad over to the house to demand an explanation. It quickly escalates into an argument. Agent McCall defends himself by saying that he was just doing his job. Melissa sides with Scott against him. When Scott starts getting too angry, Melissa pulls him away before his father can see him start to transform. Agent McCall looks curious as to why she pulls their son away so suddenly.
Agent McCall is repairing the roof at Scott's house. He is trying to rebuiled his relationship with Scott by having dinners with him. Scott keeps missing the dinners. He ends up eating dinner with Stiles and a young Derek. He accidently tells Derek information about the Hale House fire.
When Violet is brought in after attacking Scott, McCall recognizes her thermo-cut wire as the weapon used in other unsolved crimes. He knows she's part of an assassin duo called The Orphans. Agent McCall and Sheriff Noah Stilinski are going to transfer Violet to a federal facility. They are attacked by Berserkers while driving there. McCall is hurt worse, although both pull through fine.
McCall join Sheriff Noah Stilinski when the Beacon Hills High School is quarantined. When The Chemist holds Stiles at gunpoint, Agent McCall kills The Chemist to save Stiles
Time of Death
Agent McCall is seen filing a 'deadly force' report after killing The Chemist. He then explains to Scott that he will miss the first lacrosse game because he has report to the FBI Field Office in San Francisco. He also says that it's always difficult to kill someone but you learn to comparmentalize to deal with it. Scott asks him how, and he says he used to drink to do it.