NOTE: This spoiler was submitted by ThisChickyChick.
The introduction starts with a bounty hunter asleep with a cage handcuffed to his arm that is wide open. The camera shows boots, a hat, a sword, and then a female cat lying on a pillow. Puss in Boots (Antonio Banderas) is shown saying goodbye to the cat, calling her by the wrong name before he gets it right on the second try. As he is about to leave through the window, the man's skull ring catches Puss's eye and he tries to steal it. He is successful, but the man ends up waking up. He tries to catch him and throw Puss's boots at him as he escapes. The man shouts at Puss as he runs off into the desert and the female cat sighs.
Puss evades the police and goes into a rundown tavern with a lot of shady people. There are signs everywhere showing there is a bounty on Puss's head including a sign in the bar. The bar's patrons and bartender make fun of him, cracking cat jokes, and pull Puss's stool out from under him when he asks for a shot of "leche" (milk), trading in the skull ring he stole. The men in the bar know he is wanted and want to turn in Puss. Suddenly, he throws his sword at his bounty sign. When the people turn back to look at him, he is now sitting at one of the tables. One man comes up from behind him with a knife, to try to capture him, but Puss has him at sword-point, managing to cut part of two other patrons' beards off and the tie of his attacker's pants. Puss says he is looking for a job. The men say he could steal a golden statue of the Virgin of Guadalupe from the Church of St. Michael, but Puss says he does not steal from churches. They say he could steal silver candlesticks from the orphanage, but Puss says he does not steal from orphanages. Finally, one person says that there are magic beans that can grow into a beanstalk that goes to the sky. In the sky, there is a castle and in the castle there is a goose who lays golden eggs guarded by a giant. One of those golden eggs could set you up for life. Puss does not believe this at first, and it is revealed that he has been searching for a long time for magic beans and didn't think they existed. They tell him that Jack and Jill (Billy Bob Thornton and Amy Sedaris) have the magic beans.
Jack and Jill come to town in an evil-looking hog-driven wagon. Jack keeps the magic beans in his hand that is encased with a box contraption with locks. They go into an inn and ask for a room. The man at the front desk says they have no available rooms. Jack and Jill shoot one of the hotel guests and say, "Now you have one room available." Puss is on the outside of their hotel room, using his claws to cut the window open. He sees another mysterious masked cat also sneaking in. The two cats are getting ready to brawl while Jack and Jill are also arguing over the fact that Jack wants to leave their life of crime and have children. Jack and Jill spot the two cats and fire their guns at them. The two escape with Puss chasing down the masked cat. They end up at a cat tavern. Puss wants to fight the masked cat for trying to "steal" his job, but he finds out it is Dance Fight Night at the tavern so he ends up challenging the masked cat to a "dance to the death." They dance but end up sword fighting with Puss's sword getting knocked away. Puss grabs a guitar and smashes it against the other cat's head. The other cat takes off the mask, revealing a female cat, who tells him off for using a guitar to hit her in the face before going out the door into a dark alley. He goes after her, intrigued.
Puss is unable to find her but smells "something familiar, something breakfasty." The person behind him turns out to be Humpty Alexander Dumpty (Zach Galifianakis). They both feel betrayed by the other because of a past event and argue. Humpty tries to convince Puss to join him in stealing the magic beans because Puss will need Humpty's magic bean knowledge. He introduces the female cat, Kitty Softpaws (Salma Hayek), to Puss. She is able to steal anything off of anyone. She steals Puss's boots right off his feet and says "That's a lot of heel." Puss says he won't work with Humpty and leaves in a huff. Kitty says that she will convince Puss to join them. She flirts with him and tries to get him to agree, but he won't agree because of Humpty. She asks him why he won't work with Humpty and Puss tells his story.
The flashback shows Puss as a baby in a basket being sent to a children's orphanage in San Ricardo. Imelda (Constance Marie) feels an instant connection with him and takes him in. When he is sitting down to eat with all the other children, Puss meets Humpty. Humpty steals the beans from his plate but defends Puss when one of the boys tries to bully Puss for sitting in his seat. The boys go after Humpty for talking back, but Puss fights them to protect Humpty. Puss is curious about Humpty and finds out that Humpty's dream is to find the magic beans and uses his time researching everything about them. Humpty is also very smart and does a lot of inventing. Finding the magic beans become both of their dreams. They prick their fingers and put them together, swearing to be brothers. They would spend their time stealing beans with Humpty causing a diversion and Puss stealing beans, but none of them were magic beans. They would get in trouble with the Comandate who threatened them that next time they would be in jail. Imelda was like their mother, and she would be disappointed and tell them that they were "better than that." One day, Humpty is throwing rocks and one hits the lock of a wagon and an ox escapes and starts charging down the street at an old lady. Puss reacts by jumping on the ox and pulling the horns, dragging it down and managing to narrowly miss the old lady. The old lady was the Comandate's mother, and Puss becomes the hero of the town. Imelda is proud of him and gives him his first pair of boots. Meanwhile, Humpty ended up on the bad side of the law, in jail with Puss bailing him out. Puss is awakened by Humpty late at night. Humpty tells him that he is in really big trouble and needs Puss to help drive him somewhere. Puss helps drive the wagon to the place and waits for Humpty to do what he needs to do. It is only when Humpty is already over the fence that he sees the sign "San Ricardo Bank." Puss realizes that Humpty is robbing the bank and Puss has been tricked into becoming the getaway driver. He tells Humpty that he is wrong to steal from the people. By now, the Comandate and his guards see them and try to arrest them. Puss accidentally scratches the Comandate and is forced to do a getaway. A chase ensues and the wagon ends up tipping over the bridge with all the gold being thrown into the water, lost forever. Humpty is unable to get up to run and asks Puss to help him up. Puss, angry that he was deceived and unable to clear his name, tells him to "help yourself" and runs away.
It is back to the present. Humpty convinces Puss to work together with him again to find the beans. Puss agrees to do this to help the people of San Ricardo and for his mother. Kitty, Humpty, and Puss are in the mountains getting ready to jump onto Jack and Jill's wagon as it passes on the trail. Kitty jumps first onto the wagon with Puss jumping second. They have to be careful because of the sleeping baby hogs inside the wagon. Kitty uses a knife to unlock the box contraption. They end up successfully getting the beans until Puss wakes up the hogs. Jack and Jill fight the two of them. Humpty is driving a wagon beside Jack and Jill. Kitty jumps successfully into Humpty's wagon, but Puss is fighting Jill. Puss almost loses the beans but is able to grab them and jump onto Humpty's wagon. They have a wild chase with Jack and Jill using cannons to shoot at them. They get onto a broken bridge, and Humpty starts driving at full speed. He converts the wagon into a flying contraption, and they fly away. Jack and Jill stop on the end of the broken bridge, unable to catch them. They drive the wagon to the spot that the magic beans must be planted. Humpty wants Puss to have the honor of planting the beans. They water the beans and the clouds get dark and a giant whirlwind goes down onto the spot with a small bean sprout popping up. Kitty suggests Humpty speak to the bean sprout and once Humpty does, it grows all the way to the sky dragging them all with it.
They get to the top, and their voices are very squeaky because of the thin air. They play around in the clouds with Puss and Kitty having a "moment." They are interrupted by Humpty. They get into the castle but are very cautious. Humpty says that the giant died many years ago, but there is a creature there that protects the golden goose. The creature is said to be able to turn you into stone, so you must not look at it. Humpty changes into a golden suit to look more like a golden egg. They hide behind various utensils on the table before Puss and Kitty shoot a rope into this forest looking area to find the golden goose. Humpty comes after them, but they end up making too much noise and the creature comes looking for them. They hide in a log. They venture further into the forest and find lots of golden eggs lying around in the grass. They also find the golden goose that is laying eggs. They decide to get the golden goose because the golden eggs are too heavy to carry away. The creature finds out that there are intruders and give chase. They grab the goose and run back to the rope to get across to the table, but the creature snaps it. They fall onto vines over a river and continue to run with the goose in tow. Kitty ends up falling into the river and Puss jumps in to save her. They end up coming out with the river back onto the clouds. They get back to the beanstalk and use the beanstalk leaf as an air glider.
The beanstalk falls down, and Jack and Jill follow along its length to find them. Meanwhile, Humpty, Puss, and Kitty celebrate their success. Kitty and Puss dance. Puss opens up to her and proposes that when they go their separate ways, they go together. Kitty looks like she wants to be with him but is conflicted. Humpty maneuvers into dancing with Kitty and warns her not to fall for Puss and to stick to the plan. Kitty pretends to be coming down with a cough and leaves them both outside. Puss goes to sleep and gets knocked out. When he wakes up, there are vultures around him. Humpty and Kitty are gone. He sees the footprints of Jack and Jill. He goes back to San Ricardo and finds out that Humpty set him up from the beginning. He had been there all along watching Puss from the beginning and setting up his plan. He paid the men in the tavern to tell Puss about the magic beans. Jack and Jill were on his payroll, and so was Kitty Softpaws. He wanted revenge ever since Puss abandoned him at the bridge. Humpty gets the Comandate to arrest Puss. Puss is surrounded by guards. He takes out his sword to fight but Imelda beseeches him not to. Unable to disappoint Imelda, his mama, he surrenders. All the town people cheer Humpty as he gives golden eggs to everyone and Puss is taken away to jail.
In jail, he meets another prisoner, Andy Beanstalk, who tells him that the beans were taken from him by Humpty. He says that he warned Humpty that the "great terror" was the golden goose's mother, and she would destroy the town to find her child. Realizing that he is the only one who could save the town, he tries to beg the jailer to let him out. When that doesn't work, he makes his eyes big and shiny, and orders the jailor to let him out. It ends up not working, but Kitty comes to help fight. She confesses her feelings to him, saying that she "found someone more important than gold" to her. She fights off the guards so that Puss is able to go find Humpty and reunite the goose with the mother before the town is destroyed.
Mother Goose, the golden goose's mother, gets to the town and starts knocking down buildings. Puss confronts Humpty in the tower. Puss tries to convince Humpty to do the right thing. Humpty says that even if he wanted to, it's too late now. Puss says that it is never too late to do the right thing. Humpty drives the wagon with the goose to the bridge while Puss tries to lead her to the bridge. They end up on the bridge, but Mother Goose ends up destroying part of the bridge and falls down with debris on top of her. Humpty and the golden goose are hanging over the edge of the broken bridge on separate ropes. Puss holds onto the ropes, but the rope that the goose is tied to starts to unravel. Puss is forced to choose between the two, but he swears that he won't let go of Humpty. Humpty says he knows, and that's why he's going to make the choice for him instead. He lets go so that Puss will be free to save the goose. Puss returns the goose to her mother and mourns Humpty's death. As Puss looks down, there is a golden egg lying on a rock. The Mother Goose and the goose takes the golden egg back to their home.
Puss is once again San Ricardo's hero. Imelda tells him that he earned his boots. He runs into Kitty Softpaws as he escapes the town because the Comandate still wanted to capture him. They playfully banter and flirt. At the end credits, there is a dance number. Puss and Kitty dance. They finally kiss, but the kiss is not shown. Jack and Jill are shown in full body casts also dancing.
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