A 13-year-old boy named Mack disembarks from a school bus and runs home. He is a farm boy in the USA mid-west. When he gets home he sees his father abusing his mother, and then him when he tries to defend her. Mack's father is a church deacon and a closeted alcoholic. Mack walks past the house of a woman (Octavia Spencer) who offers him milk and cookies. She advises him to talk to God and that he's done nothing wrong. That Sunday at church, he gains the courage to go up to the alter and ask for prayer.
He confesses to the elder that he is sorry for not being able to protect his mother. Later that night at home, Mack's drunk of a father beats him during a rainstorm, making him recite Bible verses. Mack mixes strychnine with his booze, killing him. Cut to an adult Mack (Sam Worthington). He is married to Nan and has three children: Kate, Josh, and Missy. Flashforward, it is winter and Mack is shoveling the snow. He receives a letter in his mailbox from Papa telling him he misses him and inviting him to the shack. He slips on the ice ad has a flashback:Flashback to the family going on a camping trip.
Mack tells his children, especially his youngest daughter Missy, a story about a princess sacrificing herself to help save the people of her land. The waterfall they are looking at are the tears of the princess's father. They are singing around the campfire with another group that evening. Missy runs and tells him that he has to say his prayers to Papa his wife's name for God. He goes to pray with her, even though its not his thing. She asks many profound questions about God and the next day is drawing the princess. The canoe his other two kids are swimming in tips over and his son is trapped underneath. Mack dives into the lake to save his son as other campers help him pull him to safety.
He survives after CPR is administered. However Missy is missing. The police are called to the scene. They tell Mack that there is a man that the FBI has been after for years who abducts young girls, and he may be responsible. The town is put on alert with the FBI and community members gathered in the school gym preparing to search. He is blaming himself but his wife keeps telling him its not his fault. The Feds tell him they found a truck in the woods and they have to go, with Mack going with them. They arrive at a shack and her clothes are there with blood.
Flash forward: Mack wakes up on the ice and accuses his best friend Willie (Tim McGraw) of sending the letter. He goes to the post office, but there isn't any information. In his car he thinks about Missy's funeral. He meets with his friend and talks to him more about the note. He asks him if hes prayed about it. He thinks its a bad idea because it could be the killer trying to get him out there. He says maybe its God and insists on going with him. Meanwhile, his wife decides to take their other daughter to see her family she has become withdrawn.
His wife is afraid of losing him. He and Willie are all ready to go, the car is packed, with a gun included just in case. He goes to get his stuff and Mack takes the car and leaves without him. On the way he hears the voices of his friends and family and almost gets into an accident with a semi-truck once he hears Missy's voice. He enters the shack, gun in hand, ready to shoot in case the murderer is there.
He starts talking to him, as if he was there, yelling about how he didn't even have her body to bury, and then starts running around the shack yelling and slamming things. Again he is ready to shoot when he hears a noise, but it is just a deer. He ventures outside and sees a man. The man is very friendly, even with Mack's gun pointed at him, and invites him inside to warm himself up by the fire and tells him he has someone there that would love to see him. As he walks the snow disappears and suddenly the path and woods are beautiful and it is no longer winter. He approaches the shack and enters what is a large beautiful home. The woman played by Octavia Spencer is there, looking exactly the same as she did when he was a child. She is God (Papa) (The father), the man is her son (Jesus) and a woman named Sarayu is there also, and she is the Holy Spirit.
He leaves, thinking he is crazy, but Jesus approaches him telling him he dropped his invitation (the letter from Papa). He goes back inside and Papa tells him how much she loves him. He is surprised as she is a woman she tells him that he couldn't handle a father right now, so she took on that appearance instead. He asks her why she forsake him, and where she has been. Over dinner he tells them that his son is doing well and has a girlfriend, but his daughter not so much. They talk to him about how much they love him and want to get to know him, even though they already do.
While he sleeps he has visions of his daughter being kidnapped. In the morning he talks to Papa over breakfast about how she punishes people. However she tells him no, sin is punishment enough, and everything she does works together for good. He accuses her of lying, due to all the pain and suffering in the world. However she tells him the reality is that he doesn't see the whole picture. He doesn't believe she is good but he has to learn to trust her.
However he says there is nothing that she could say that would justify Missy's death. He gets up and leaves into the woods, but Sarayu approaches him with directions to his truck and the keys. She tells him they aren't justifying anything, but are there to help heal it. She tells him she needs help in the garden preparing for the next day. She tells him that the poisonous plant, when combined with the right plant, contains healing powers. After a long conversation with her, Jesus tells him he can take the boat out if he wants.
His boat starts to sink as he has flashbacks to the day it all began. Jesus keeps telling him not to panic and to look at him as he walks on water. None of it can hurt him as long as he keeps his eyes on him he isnt going anywhere. Suddenly the boat is back in one piece and everything is fine. He tells him they need to go, but Mack insists he will sink.
Jesus assures him he wont just trust him. After they get back on land, he tells him to follow the path and will wait for him there. He enters and meets Wisdom(?). They talk about judgment ad she tells him that HE is the one who judges every one based on their clothes, appearance, etc. She tells him he has to judge people and sits him down. He sees visions on the wall of his mother and he getting beat by his father and then sees a vision of his father as a little boy getting beat.
Cut to him seeing the visions again of his little girl being taken away. She asks him if God is to blame and he says yes. She says if it is so easy for him to judge God, that he must choose one of his children to go to Heaven and one to Hell, since that's what he believes God does. She gives him reasons why he could pick either one. He tries to leave saying it isn't fair and he cant choose, but she keeps saying he must. He says that he will go to Hell instead of them and take their place.
She tells him that's what Papa goes through. There's no such thing as a pain free life, and as long as there is free will evil will be invited in. He sees visions of Missy playing and blowing him a kiss and then running to him. He asks if Missy forgives him for not saving her. She tells him that she never felt that way.
Back at the beach he and Jesus run through the water. That evening all three of them take him to the top of a hill. Sarayu covers his eyes and when he opens them he sees people glowing as they see people in color and light. One is walking towards them its his father. He apologizes to Mack and says he was blind and couldn't see anyone. Mack says he was scared and they forgive one another.
In the morning Papa comes to him, now as an American Indian man. He brings him to the woods and wants Mack to forgive the killer. He says he wants to hurt him, and he wants God to hurt him also. He tells him that he too is his son, and he wants to redeem him. Mack says he should burn in Hell, but Papa reminds him that he is not the judge. He guides him into forgiveness, and tells him its ok that he is still mad, and it will get easier in time.
He is led to her body which he wraps and carries her back to the shack. He asks Jesus to take her as he cant, and they put her in a coffin and bring it to the garden for burial. Beautiful flowers grow above the ground. He is ready to go home, however they tell him that he needs to talk to Kate, as she blames herself for Missy's death. He tells them that he still wants them in his life. Suddenly it is winter again. On his way home he is hit by the truck and winds up in the hospital.
Willie is there and tells him that he never made it to the shack and was hit by the semi that night on the way there. His family comes into the room and he tells Nan that he saw Missy and shes beautiful. He talks to Kate and tells her nothing is her fault she feels it was her fault because she stood up on the boat causing it to tip over in the first place. He tells her she doesn't have to go through it alone. His life turns around and they are able to once again have a happy life..