Prior to the film
Before the events of the film, Yates worked at a desk, before one day being asked to temporarily take over a fraction of the CIA for a couple months. Somehow, he managed to make his promotion permanent, much to the ire of his former supervisor Victoria Lasseter.
In the film
By the events of the film, Yates has become a corrupt CIA Agent, clearly letting his position go to his head. He is seeking to rid the world of the Ultra Program (a program of third strike minor offenders being given a second chance to do something with their lives by becoming living weapons) in order to prove the program is a failure while proving his Tough Guy Program (training mentally ill people to become assassins) is a success. By doing so, he hopes to receive a massive promotion.
Upon finding out that Mike Howell (the Ultra Program's only surviving member) keeps trying to leave his town of Liman, West Virginia, Yates decides to terminate Howell. When Lasseter tries to point out Mike has the right to do whatever he wants, Yates berates her, reminding her that he is now her superior and has the right to make whatever call he feels necessary.
Yates sends two assassins to plant a bomb on Mike's car, but he sees them and, thanks to Lasseter activating him, manages to kill them both.
When Mike and his girlfriend Phoebe are arrested because of the murders, Yates sends Crane and Laughter to kill Mike. The police station is destroyed, but Mike manages to kill Crane while Laughter escapes.
After realizing that Lasseter is in the town, Yates blocks the town in, claiming Lasseter had intercourse with sick monkeys, leading to the spread of the contagious disease "Super Typhoid" as a cover. He then meets with Laughter (now missing his teeth) and the other members of his Tough Guy Program, giving them the orders to do whatever it takes to eliminate Mike. He also calls Lasseter's former assistant Petey, who has been helping Lasseter, and threatens him with treason if he continues to help her.
Yates then sends two assassins to Mike's friend Rose's house, where Mike and Phoebe are hiding out. Though Rose and his two friends are killed, Mike and Phoebe escape. However, in the process, Mike discovers that Phoebe is actually his handler, causing a rift between the two of them. This allows Laughter to kidnap Phoebe and attempt to kill Mike by lighting his car on fire, but he is secretly saved by Lasseter.
Phoebe is then brought before Yates, who taunts her about giving up a future as a CIA agent in order to be with Mike. He promises her that she will be arrested, before discovering that Mike is still alive. This prompts him to call Petey and order an airstrike, which would result in massive damage. At the last second, Petey stops the drone strike and secretly calls Yates' supervisor.
After the two agents sent in to kill Mike at his home are killed, Yates calls Mike in order to talk to him. Though at first Yates goes along with Mike's promise that he will surrender and stop trying to kill him, he quickly gets annoyed by Mike's stupidity, prompting him to threaten to kill Phoebe if Mike does not give himself up.
Once Mike appears, he attacks Yates and his subordinates of the Tough Guy program using an excessive amount of fireworks, and then kills almost all of Yates's men, but spares Laugher after the latter reveals that he was turned into what he became forcibly by Yates. Yates escapes the violence into the hallway, planning to use Phoebe as a hostage to control Mike, then all of a sudden he was grabbed and strangled with a cable to within an inch of his life before being stopped by Agent Kruger, who takes both Lassiter and Yates into the forest, before shooting Yates dead.
Yates is cruel and uncaring, shown when he was willing to destroy the entire town of Liman just to take out Mike. He was also very cocky, as he believed that he wouldn't get in trouble for all he had done.