Dora The Explorer is now a teenager, and her parents Cole and Elena are making her live in the city with her cousin Diego so that she can have a normal life. Although she is excited for a new adventure, she finds that high school is tough, and not everyone is willing to be her friend.
On a field trip, Dora and Diego, plus classmates Sammy and Randy, are kidnapped by mercenaries and taken to the jungle in Peru where Dora used to live. Swiper the fox steals Dora’s map that will lead the mercenaries to the fabled Incan city of Parapata. The kids are found by a man named Alejandro, who claims to know Dora’s parents. As they search for Cole and Elena through the jungle, they are helped by Dora’s best friend, Boots the monkey.
After finding Dora’s parents, they learn Alejandro is the villain and that he has been leading the mercenaries to find Parapata. Boots helps the kids escape the mercenaries, but Alejandro follows them since he knows Dora will figure out how to get to Parapata. They eventually find the place and are met by Princess Kawillaka and the Lost Guardians, who protect Parapata. Alejandro’s greed for their treasure leads to him being taken as their prisoner, but Dora convinces Kawillaka that all they want is knowledge to document from Parapata. Before they can do so, Swiper steals a golden monkey totem, causing the place to collapse. Dora and Boots stop him and save Parapata.
Although Cole and Elena invite Dora to join them on another adventure, Dora has decided to stay with Diego and their friends.
Deep in the Peruvian jungle, Dora, daughter of explorers Cole and Elena, spent her days going on adventures with her monkey friend Boots, her cousin Diego, and imaginary friends Backpack and Map while thwarting the fox thief Swiper. When they were both six year old, Diego left to his family in Los Angeles, while Dora’s family remained searching for the hidden Inca city Parapata.
Ten years later, Dora’s parents decipher the location of Parapata but chose to send Dora to Diego’s school in LA while they travel to the lost city. Staying with Diego’s family, Dora meets fellow students Sammy and Randy, but Diego considers her an embarrassment. On a class field trip to the museum, Dora and the others are lured to its off-exhibit archives, where they are captured by mercenaries who fly them to Peru. When they land, a man named Alejandro, who claims to be a friend of Dora’s parents, helps them escape. In the the process the mercenaries, aided by Swiper, steal Dora’s map. Alejandro reports that Dora’s parents have gone missing, and that the mercenaries are searching for them in hopes of getting into Parapata and stealing its treasures. Dora resolves to find her parents first with Alejandro’s help, while the other teens come along in hopes of finding rescue.
The group travels through numerous obstacles, including quicksand, Inca ruin puzzles, and attacks from forest guards of Parapata. After numerous hazards, Dora reaches her parents just outside the borders of Parapata, but Alejandro reveals he was working for the mercenaries all along and captures them. The other teens are caught as well, but Boots the monkey helps them escape. With Dora’s parents still prisoners, the teens decide to find the way inside Parapata in hopes of acquiring treasure that they can use to bargain for Elena and Cole’s release.
Inside the hidden city, Dora and the others solve its temple’s puzzles and dodge its traps, bringing them to the center shrine. Alejandro turns out to have been following them, and attempts to steal its central idol himself, but instead falls into a trap. The soldiers guarding Parapata, led by their queen, defeat the mercenaries and confront the teens, but Dora speaks to them in Quechua, assuring that the teens only came for her parents and to learn. The Inca allow the teens and Dora’s family to leave, allowing them a glimpse of their greatest treasure.
The teens and Dora’s parents arrive at Dora’s jungle home. Her parents discuss going on another expedition as a whole family, but Dora decides to return to school. She and the other teens celebrate at a party while Alejandro and the mercenaries remain prisoners in Parapata.
In a Peruvian jungle, little Dora the Explorer (Madelyn Miranda) and her cousin Diego (Malachi Barton) are having an adventure with Dora’s best friend, Boots the monkey (Danny Trejo). Afterward, the two have dinner with Dora’s parents, Cole (Michael Pena) and Elena (Eva Longoria), both of whom are professors. They tell the kids the legend of Parapata, a lost Incan city said to hold a great treasure. However, Cole and Elena would rather learn more about the city’s history than to take the gold.
Dora and Diego go to bed, but they are sad since Diego must go back home with his family. In the morning, the cousins bid each other farewell, but Dora chases after Diego’s parents’ car.
Ten years later, Dora (now played by Isabela Moner) is still adventurous and cheerful. She and Boots are being chased by pygmy elephants before encountering crocodiles. They then come across a cave with Incan carvings. Dora then spots a golden totem that she thinks holds a clue to finding Parapata. She tries to leap across the huge gap for it, but she ends up falling with no injuries. Boots goes to get Cole and Elena, and they take the totem with them. They all see that there’s a map on the back that can lead them to Parapata. Unfortunately for Dora, her parents tell her that they are sending her to live with Diego (now played by Jeff Wahlberg) and his family to go to school and live like a normal kid. Dora is dismayed but goes along with it, although she is not allowed to bring Boots with her.
Dora leaves her parents and arrives in the big city, greeting everyone she meets. She finds her aunt and uncle and then excitedly greets Diego, who has now become more aloof and somewhat cynical. The two start school together, where Diego warns her that it will be like nothing she has encountered before. Upon arriving, Dora passes through a metal detector and has to empty her backpack, which contains things like a road flare, a knife, medication, and a yo-yo. She also meets the class honors student Sammy (Madeleine Madden), whom Diego considers to be snobby, and then Randy (Nicholas Coombe), a nerdy kid that instantly develops a crush on Dora when she shows her knowledge of astronomy. In class, Dora upstages Sammy with her educated response on the teacher’s question about “Moby Dick”, which upsets Sammy.
Over time, Dora maintains her friendly disposition while getting used to school. She tries to keep in touch with her parents, but they eventually stop responding. She then attends a winter dance where everyone is dressed up as their favorite stars (as in, celebrities), and Dora dresses up as the sun. She starts to dance in front of everyone by mimicking animal movements, and when she invites Diego to join, he is just embarrassed in front of everyone. Dora follows him outside, but he tells her that she is the class weirdo. This hurts her feelings, and she runs home where Abuelita Valerie (Adriana Barraza) comforts her.
The next day, the class goes on a field trip to a museum where they go on a scavenger hunt. Dora and Diego are left with Sammy and Randy. A security guard calls Dora over and offers to help. She lets Dora and her friends go down to the storage room where they are found by a mercenary named Powell (Temeura Morrison). He and the security guard (plus a third man) lock the kids in a crate, and Powell tells Dora she is going to lead them to her parents so that they can find Parapata.
The kids wake up in the crate. Dora takes her knife out to open it and then realizes they are in Peru. She thinks someone has spotted her, but they are found by a man named Alejandro Gutierrez (Eugenio Derbez), who claims to know Dora’s parents after working with them at the university. He breaks the kids out, but Powell and his goons spot them. He orders Swiper the fox (Benicio Del Toro) to go after them. The group runs toward a hangar, but Swiper catches them and…well, swipes Dora’s map out of her backpack. He gives it to Powell, but Alejandro rides up in a van to get the kids. The mercenaries chase after them, leading Alejandro to hide them out in a crop field.
Dora tells the group they should go find her parents. Alejandro produces Cole’s journal that he claims he found as he was tracking them before they disappeared. They drive until they reach Cole and Elena’s car, but they don’t see them there. The group must then walk through the jungle over a day, where Alejandro tells the kids about Los Guardianes Perdidos/The Lost Guardians, a dangerous ancient militia dedicated to protecting Parapata. Dora also shows a knowledge of the Incan language. The group then finds Cole and Elena’s campsite, but they are not there and the place is trashed. They are then found by Boots, whom Dora is elated to see. She then thinks she can track her parents before the mercenaries get them.
The group continues walking, but Sammy has to poop. Dora helps her find a spot to go privately, even making a song about it. Arrows then start flying as the Lost Guardians fire them while remaining hidden. The group runs and hides in a log, but it gets knocked over and they roll down a hill. After getting to safety, Dora is bummed out over the situation, plus Sammy’s frustration over her. Diego goes to talk to her, but Dora starts to realize that he actually has a crush on Sammy, which makes her gleeful.
The group spots the mercenaries, but Boots distracts them to make sure nobody spots the group. Dora realizes that the mercenaries are headed in the opposite direction of her parents, since they had written that the passage to Parapata is through the ruins of an old opera house. As they continue on their journey, they step in quicksand. Dora helps her friends get out by relaxing themselves before swimming out, but Alejandro panics too much and sinks faster. It doesn’t help that two scorpions start mating on his head. He ends up sinking all the way, but Randy sees that his legs are sticking out from under a rock. The kids pull him out alive.
They are then found by an old woman (Isela Vega). She takes them into her home, but she reacts badly when she hears Parapata mentioned. Using stone figures, she implies that the group will die if they try to find Parapata. She does offer to take the group downriver to get them home, but Dora decides to continue finding her parents. Diego and Alejandro go with her, so the old woman takes Sammy and Randy with her. Just before the two board the boat with the old woman, Sammy notices her wrist tattoo being the same symbol found on the arrows shot by the Lost Guardians. She and Randy run off to warn the others.
On their walk, the trio comes across giant flowers. Alejandro accidentally brushes one and they all start to produce spores. The trio start to hallucinate and see themselves in the art style of the cartoon (complete with talking Map and Backpack). Alejandro takes his clothes off as he loses his mind, but Dora and Diego spot a way forward. They leap across a canyon and are caught by Sammy and Randy. Dora comes back to Earth as she regains consciousness. The group sits around a campfire, where Diego tells Dora that he never forgot about their adventures.
After waking up, the group proceeds forward, but they fall through the ground and end up in an aqueduct. Randy pulls a lever that causes the place to start flooding. As the water level reaches the top, he remembers he can hold his breath for up to seven minutes, so he swims down and finds the hatch to release the water. The group is sucked down the drain, and they come up to a river where they find Cole and Elena. Dora happily reunites with her parents, but when she mentions Alejandro, they say they don’t know him. It turns out Alejandro was leading the mercenaries and had tricked Dora into leading him to Parapata. Powell and the others come to take the group and force them to lead them to the city.
The group eventually spots Parapata from a distance, but they must continue to find the entrance. Boots frees the kids from their ropes, and Dora knocks out a merc with the yo-yo. Dora runs to find her friends and ends up stumbling down a hill. Boots finds her, and she expresses doubts in herself since she feels she got them all into this mess. Boots then speaks for the first time to give Dora encouraging words. The others find her and agree to help her get her parents back.
The kids find Swiper and Powell guarding the gate that leads into Parapata. Dora throws a golden poison frog, which knocks them both out. They then see that the moonlight illuminates the tiles on the ground, but four specific ones remain lit. They match the constellations to their animals, and they pull the levers that open the gate entrance. It brings them to a room where they must shine a light to get another passage to open. Sammy gets freaked out by spiders, causing her to drop her bowl with the light, and the spike-covered ceiling starts coming down. The kids get out before they are crushed. They then end up in a room where they accidentally step on the wrong tile, causing them to slide down the floor. They all jump before falling onto spears, and they make it to safety.
They finally come across the treasure of Parapata, but Dora knows that there must be some kind of test. Alejandro appears, as he had been following them. Dora reads the Incan inscription and sees that the golden monkey totem requires a gift of what the Incans valued the most. Alejandro is certain that it’s gold, so he places a gold coin on the monkey’s hands. A rumbling happens, and the floor beneath Alejandro drops, and he falls through, but holds on for his life. The Lost Guardians emerge with Cole and Elena, as well as the old woman. She raises her hand, and her true image is revealed – she is Princess Kawillaka (Q’orianka Kilcher). The Guardians take Alejandro as their prisoner, but before they do the same to Dora and her friends, she speaks in Incan to Kawillaka to prove that they don’t want the treasure, but rather the knowledge. She pours water into the monkey totem’s hands, which reveal the true treasure behind the walls to Parapata. Swiper ruins the moment by swiping the monkey totem, causing the whole structure to start coming down. Everyone runs to safety, but Boots knocks Swiper down, and Dora returns the totem to its place. Cole and Elena show Dora how proud they are, and Diego and Sammy acknowledge their feelings for each other with a kiss.
Everyone returns to Cole and Elena’s home for dinner. They sit by the water with Dora, telling her that they are going on another expedition and would like to invite her. Although she is interested, Dora has decided to stay in the city with Diego and their friends. As she walks away, Cole and Elena start crying hysterically.
During the credits, Dora, Diego, Sammy, and Randy all do a song and dance at school, leading all their classmates to join. Meanwhile, Swiper tries to take the totem that Cole and Elena have, but they stop him with a “Swiper, no swiping!” (“Aw man!”)