On a rare trip home, Sam is in shock when he learns that the leader of the Liberation army has been killed when his helicopter crashed on the way to the peace talks in Russia. Unable to relate to his family, he shouts at his wife and daughter, and turns poor Donnie away.
He is more animated and fervently preaches at his church, frustrated by what he sees as apathy by others who haven't witnessed the murders he has seen.
It's not long before Sam hears about Donnie who OD'd without his friend to support him. At the service Sam feels deserted by God. He sells everything he owns, including the business, and puts the money back into his orphange projects. Lynn begs him not to, but he doesn't listen.
He flies out to the Uganda/Sudan border a different man. The others at the orphanage are frightened by him when the boy with the scar accidentally pours something hot on his arm, and is pushed away aggresively in the chest.
Armed with his machine gun, he protects the female aid worker whose convoy is stopped on a bridge by the LRA, but not before she is beaten with a rifle by one of the soldiers. Sam shows up and guns down the enemy without remorse. Even his friend Deng is surprised by the change in 'The Preacher'.
Sam retreats to his outhouse that night, alone, and looks at a gun in his hands to think about a way to end it all. The boy with the scar knocks, walks in and sits next to him in silence. After a long pause he softly tells Sam about what happened and that he was forced to murder his own mother by the rebels. But then he surprises Sam and says that you can't live with hate in your heart, and you need to learn to forgive.
Next morning, Sam walks outside to survey all that he has done and helped to make a difference. There is a football in the middle of the field. He starts to kick it around and suddenly all the kids run over to play. Happiness is back in the camp.
Sam phones his daughter and patches things up with his family back home.
As he shows the kids a video of his daughter, there is word of an LRA convoy that has been spotted. They track it - and then pull out an RPG to take out the lead vehicle! They gun down the rest of the soldiers. When they open the canvas to the largest truck, inside are a number of frightened children. They pack their own vehicles with the kids, while Sam is going to stay behind this time and protect those they can't take until his people can return.
In the closing titles we see that Amnesty estimate that Kony and his LRA are responsible for over 400,000 murders and 40,000 child abductions. Sam continues to fight. Sam and Lynn are still together.
In the end credits we see the real Sam Childers, Lynn and Paige. We see real footage from the atrocities and hear from Sam as well. He defends his actions to fight back - and says that if your son or daughter was kidnapped, and he could get them back home safe, would you care how he did it?