Kristen, David and Ben continue to assess cases that involve wayward technology, possessed pigs, demonic oppression and infestation, a dance muse conjured by alleged witches and an evil relic. Throughout, Leland attempts to lure Kristen into raising a baby antichrist who was conceived with her ovum. David is recruited by the Vatican's secret service to "remote view" a paranormal ability to see the unseen in order to detect evil. Ben is hit by an ion beam, causing him to see visions of a taunting jinn until he discovers an unusual solution to banish it. Finally, all three realize they only have a few weeks left to assess cases because the parish has decided to disband the team due to a lack of funds. This culminates in one last confrontation with Leland and the 60 families that make up Evil in the modern world.

Season three of Evil begins moments after the end of season two: when a newly ordained David and Kristen kiss. The two not only have to navigate this fraught new reality, but contend with David's involvement with "the entity", an espionage unit within the Catholic church. Meanwhile, Ben finds his brain breaking from their unsolved cases and turns to his sister for help.

The second season brings evil closer to home. Kristen struggles with her darker nature, while David suffers temptation as he gets closer to his ordination. Meanwhile Ben is visited by night terrors that prey on his greatest fears.