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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.

Orphaned

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. 

Weaponized

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.