The movie begins on the Mississippi River in Arkansas, where two teenagers, Ellis (Tye Sheridan) and Neckbone (Jacob Lofland) are on a small boat. They arrive on an island, and set a timer on their watches to remind them when to get back on the boat. The boys search the island, stopping only to smash a cottonmouth snake with a rock, eventually finding what Neckbone had promised: A medium-sized boat stuck in a tree, 20 feet off the ground. The boys climb the tree and explore the boat, dreaming about getting it down, fixing it up, and making it theirs. A search of the boat's cabin reveals some adult magazines and some fresh food rations. Ellis realizes someone is living in the boat. The timer goes off, and the kids retreat to their boat.
Upon arriving back at the shore, they discover footprints and realize someone has visited their boat. Mud (Matthew McConaughey) reveals himself, fishing and smoking a cigarette. The three exchange banter, with Neckbone fully distrusting Mud, but Ellis becoming intrigued, particularly after they determine that they know some of the same people in town. Mud says he's waiting for someone, and if the boys provide him with food while he waits, the boat is theirs. Ellis agrees, and the boys get in their boat and head home.
Ellis shows up at his Dad's business later than he had intended. His father (Ray McKinnon) is curt, but understanding. The two fill the back of their truck with fish and head out on the town to make deliveries. At the end of the day Ellis receives $5 for his help. They head back home, which is a crude houseboat on the Mississippi River. Ellis' parents clearly have a strained relationship. When his parents go to bed, Ellis fills his backback with canned goods from their cupboard.
The next day, the boys return to the island with food for Mud. He is grateful, and the two groups swap stories. The boys notice that Mud keeps a gun in his pants and become alarmed. Mud says that he only has two things for protection: His shirt and his pistol. He tells them that they have nothing to fear from him. He goes on to tell them who he's waiting for: his woman, Juniper. He describes her beauty in detail, all the way down to the tattoos on her hands: a pair of swallows. They boys leave the island.
The next day. the two boys are sitting outside Neckbone's trailer, discussing the merits of Mud and the boat in the tree. Inside the trailer music plays, as Neckbone's Uncle (Michael Shannon) has sex with his girlfriend. The boys' discussion is interrupted when the girlfriend comes flying out of the trailer, upset with the uncle for trying to do something "ungentlemanly"... As she escapes to her car, she stops to tell Ellis and Neckbone to always treat a woman like she's a Princess, but the boys are too distracted by her cleavage to hear a word she says. The girlfriend departs, as do the boys.
Later, the boys are at a gas station across from a Piggly Wiggly Supermarket where all the high school kids are hanging out in the parking lot. Eventually an older boy gets a bit too physical with his girl (Bonnie Sturdivant), and she protests. Ellis comes flying across the street and slugs the boy in the face. As the boy retreats, Ellis and the girl, May Pearl, exchange pleasant flirtations, despite the fact she is several years older. She invites him to look her up. Their conversation is interrupted by Neckbone's sighting of of hot woman (Reese Witherspoon) exiting a nearby hotel and entering the supermarket. The two quickly follow and watch her from within the store. Ellis notices a pair of swallow tattoos on her hands and realizes that this is Mud's woman.
The next day back at home, Ellis' neighbor Tom Blankenship (Sam Shepard) is sitting on his roof, sniping cottonmouth snakes in the river with a pellet gun. Another conversation between Ellis' parents becomes heated, and it's clear that their relationship is nearing a breaking point. Ellis departs and returns to the island with more rations, as well as news of Mud's woman. Mud is elated, and he writes a note for Ellis to deliver to her.
The following morning, the boys devise a plan to find Juniper's motel room. They load up Neckbone's dirtbike with fish, and start going door-to-door at the motel, pretending to sell fish. Several doors into the effort, they come across her motel room, the door open, with a mafia-style gentleman named Carver (Paul Sparks) beating her up on the floor asking for the location of Mud. Ellis rushes in and immediately gets slugged in the face. Before Carver can finish pummeling Ellis, Neckbone enters with two bags of fish, exclaiming that they're just selling fish. Carver stops his assault and exits. Juniper is grateful for Ellis' help, and is shocked when he gives her the note from Mud. She passes on a message to give right back to Mud.
Fade to the next day, the boys make the delivery and tell Mud about the incident. Mud tells them to be very careful, but to please keep an eye on her. Upon returning home from Mud, Ellis looks up May Pearl in the phone book and asks her on a date. She agrees. They go to a bonfire later. He gives her a little bracelet and they make small talk before she gives him a little kiss. Ellis believes he now has a girlfriend, and is quite pleased with himself. Upon returning home, Ellis' father is waiting for Mud on the porch. He is drunk, and he tells Ellis that he loves him before revealing that his Mom wants a divorce. They're going to lose the houseboat, and she's moving to an apartment upriver. Ellis is devastated. He sneaks out of his bedroom and takes the boat to see Mud. Ellis makes his delivery and the two sit and talk about life and women in a very touching scene. Mud gives lots of good advice about love.
On to the next day, Ellis is on a car ride with his mother, having an awkward conversation about the divorce. Their discussion is interrupted by their arrival at a police road block. They're looking for a dangerous fugitive, and as you might imagine, the picture of that fugitive is clearly Mud. Ellis and Neckbone race back to Mud to call him on his past. Mud reveals that he killed a man who threw Juniper down a flight of stairs, causing her to lose her unborn child. The man who was roughing her up is related to the thug who roughed her up in the motel. Mud decides that there's a change of plans. He's keeping the boat since he can't escape by road. He needs the boys' help to get her down and get her running again. Neckbone asks what the kids will get in return, and Mud offers his pistol. The boys agree. Mud's next request: Go get Tom Blankenship for help. Mud calls Tom Blankenship a CIA assassin, and tells the boys that he should be able to provide aid.
The boys float over to Tom's, who is taken aback by the mention of Mud. He gets on the boys' boat and heads to the island. Once there, Tom berates Mud like a father to a son, telling him that the girl is the source of all his problems, and that he'll get no aid from him. Tom storms off, and upon being deposited back at his houseboat, tells the boys to stay away from Mud.
Cut to another day, where Ellis is helping his father load the truck with frozen fish. Ellis becomes distracted at the sight of three cars with Texas license plates pulling into a nearby motel. One is Carver. Ellis gets back to work, and the camera switches to inside the motel. Carver is joined by his father, (Joe Don Baker), who is also the father of the man Mud killed. There are roughly 8 other thugs in the room. The father asks them all to gather around and take a knee, declaring "It's time to say a prayer for the death of the man who killed my boy."
Later on, the boys are back at the supermarket, starting to gather requested supplies. Ellis sees his girl, May Pearl and calls to her, but she pretends she doesn't see him. They are interrupted by Carver, who starts to grill them on their relationship with Mud and Juniper. He offers to pay $40 for the fish, but Ellis declines. The boys depart and continue to scavenge. Tom sees them load a chainsaw and some supplies onto the boat. The boys head to Mud and give him the supplies. While the three of them talk, we learn they are being watched from a distance. It seems that Neckbone's uncle has followed them out. He silently watches.
The next day, Tom sees Ellis about to depart and calls to him. Ellis comes over and Tom tells him that he knows he's going to go see Mud. Ellis asks about Tom's CIA past, with Tom telling him that it's all a bunch of hogwash. Tom says that Mud isn't who you think, and that he's gotten into all of this trouble because of a girl who doesn't even want to be with him, who probably set him up. He warns Ellis not to mess with Mud, but Ellis blows him off and exits.
Cut to a montage of Ellis and Neckbone collecting scrap throughout the town and bringing it to Mud. Things are going quite well. One night Tom leaves a bottle of whiskey for Ellis to take to Mud. He obliges. Back on the island, Mud has had tremendous luck with the boat. It's out of the tree, but still needs more work. Mud tells Ellis that it's time to get Juniper out of there. They devise a plan.
Later on, Neckbone and his uncle are on a fishing boat, the Uncle is prepping his makeshift scuba gear--he makes money pulling clams out of the river. The Uncle asks Neckbone if he was in any trouble, assuring him that he would help. Neckbone says everything is fine, playing it all very cool. The Uncle lets the whole thing drop. Back on land, Ellis is at Juniper's motel room. He tells her the plan. Tomorrow at 5pm, meet him behind the motel. She hesitates, then agrees.
The following day the boys are preparing for the great escape. They're in Neckbone's trailer, where the Uncle is hinting that he knows what's going on, and is warning the boys to either stay far away from trouble, or "go out and get your tip wet". The boys leave, heading for their mission. They arrive at the motel. No Juniper. Her room is empty, so the boys ask the manager if they saw her leave. He tells them she went to a bar down the street. The boys pursue. Upon arriving at the bar, the boys blend in for a few minutes, ultimately finding Juniper hugging a man who is kissing her on the neck. Juniper makes eye contact with Ellis, and a mildly shocked look appears on her face. The boys are thrown out of the bar. They decide that they have to tell Mud. Nighttime has hit the island. Mud tells the boys that it's time to get a motor. They think they know where to get it. The boys break the news about Juniper. Mud is devastated, but keeps it together. He crafts a note to give to her. The boys leave.
Fade to the boys at a scrapyard. They find an old abandoned boat motor, and debate whether or not to take it. They decide nobody will miss it, and drive off on their bike with the motor in tow. Ellis now has a solo mission. He goes to Juniper and gives her the note. The note tells her that it's over. She asks that Ellis tell Mud that she understands. When Ellis presses Juniper about why she did it, she tells him that she just couldn't spend the rest of her life with him, on the run. Ellis is disgusted and leaves. As he's walking away, he turns around and looks through her window to see her crying on the bed. He leaves again.
They take the motor to Mud, who is now topless (for the ladies in the audience). He says it will do, and starts work on getting it all rigged up.Once back at home, Ellis calls May Pearl and gets her mother. He asks if she's been receiving his calls, and continually asks to talk to May Pearl. Just as he's about to talk to her, Ellis' father storms into the room and slams Ellis against the wall. He tells Ellis that a friend of his saw Ellis and Neckbone steal that motor from their neighbor's yard and they are all incredibly upset about it. He screams at Ellis for stealing a man's livelihood and demands he return the motor and apologize. Ellis says that he can't, and he'll offer to pay for it. Ellis' mother steps in before things get more physical, and Ellis departs.
Mad at the world, Ellis is driving through town on Neckbone's dirtbike, when he spies May Pearl parking in a car chatting up an older boy. Ellis approaches, asking her why she hasn't called him back. The older boy interjects and Ellis slugs him. This time the older boy gets out of the car and start pummeling Ellis until May Pearl stops him as a crowd gathers. Ellis calls her his girlfriend, a fact May Pearl adamantly denies, and joins the group in belittling Ellis. He leaves.
Later in the day, Ellis and Neckbone arrive at the island, Ellis fuming at Mud. He decks Mud and calls him a coward, crying and saying that everything Mud told him about life and love was all a lie. Ellis then storms away, Neckbone giving chase to try to talk some sense into him. Suddenly Ellis falls into a pit and is knocked out. Neckbone runs to find Ellis covered in cottonmouth snakes. He calls for Mud, who throws his shirt back on and runs to the pit. He scoops Ellis up and races him to Neckbone's boat. The three speed off with Mud checking Ellis for snakebites. He finds one. They have to get Ellis to a hospital.
Arriving onshore, Mud takes Neckbone's dirtbike and speeds Ellis off to a hospital, taking him into the ER. After safely depositing Ellis, the attendants ask Mud for information, causing him to freak out at all the people looking at him. He runs out of the hospital. The attendant finds a picture of Mud on a flier and calls the police. Fade to the mafia father getting a call at the motel.
Fade to Ellis recovering safely at home. His parents are loving on him and all seems forgiven. Ellis has no idea how he got off the island or back home. His dad tells him that a strange man brought him in. Ellis knows it was Mud. Back in town, Juniper smokes a cigarette on the balcony of her motel. She notices Mud watching from a distance. The two share a glance. She barely waves at him to acknowledge him. He waves back, as if saying goodbye, then walks off. She is left smoking her cigarette and looking down at the ground.
Slow fade one more time to a nighttime scene. Back on the island Mud and Neckbone drop the boat in the water. She floats, and the job is done. Mud keeps his word and surrenders his pistol to Neckbone, keeping the bullets for himself. Mud laments that Ellis isn't there to see this. He then tells Neckbone he needs one last favor.
Mud quietly arrives at Ellis' houseboat. He sneaks in the window of Ellis' bedroom. He lets him know that he loves him and everything will be okay. Meanwhile, bad guys are sneaking towards the houseboat, guns drawn. Mud and Ellis continue to share their tender moment, until gunshots blow holes in the wall of the houseboat. Everyone is unharmed, but the assault continues several seconds later. Mud hides Ellis under the bed, while his parents take shelter in a closet with a revolver. One assailant enters, Mud knocks him out and takes his weapon. Now we have a shootout. Mud gets the advantage until a thug sneaks behind him and prepares to shoot--until his head explodes. Cut to Tom Blankenship reloading a sniper rifle across the river. The good guys now have the advantage, particularly after Tom snipes Carver, killing him. Just when it looks like the good guys have won, a thug appears out of nowhere and shoots Mud as Mud leaps into the river. The thug is quickly dispatched by Tom.
Ellis saw Mud get shot, and ran screaming his name to the river's edge. He screams his name into the night. Fastforward a few hours, police are now at the riverboat. An office calls the unnamed mafia father and informs him that his other son has been killed. He hangs his head in sadness in the hotel room. Fade to Neckbone's uncle, under the water collecting clams by lamplight. He looks up and sees the silhouette of Mud's body float by on the surface.
Fade to a day at some point in the future. The government is tearing apart the moorings of the old houseboat. Ellis' old home floats downriver. Neckbone and Ellis watch from up the road, where Neckbone has fixed his bike. Ellis' Dad arrives and takes Ellis away, eventually dropping him off at his Mom's new apartment. His Dad says he'll see him next week and to be good to his mother since this is hard on her too. Ellis spies a group of young women and smiles at them. He's okay with this new life, and he heads inside.
Cut to Tom Blankenship, piloting the restore boat down the river. He heads below deck, where a recovering Mud is laying face down with a bandage on his back where he was shot. Tom says "Son, you need to see this." They head above deck where they see the boat is about to hit open water. They're free. Mud smiles. Cut to black.
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