A young woman's voice says that she was once told the beings in the forest rely on the help of others for the good of the forest. If you don't believe it, you ought to look closer. As we move through the forest, a security camera catches three crows surrounding a hummingbird. A man, Professor Bomba (Jason Sudeikis) runs in to see what's happening, along with his headgear. The hummingbird falls to the ground, but Bomba finds it and notices it is carrying a saddle.
The rider of the saddle, Nod (Josh Hutcherson) is running from the creatures on the crows, known as Boggans. Coming to his aid is Ronin (Colin Farrell), a Leafman warrior. Ronin takes out the Boggans, even though Nod acts like he had it under control.
One Boggan falls and gets splattered on the windshield of a cab. We meet Mary Katherine, aka MK (Amanda Seyfried), who is going to see her father. She implies to the cabbie that their relationship is a bit strained. She gets to the house, which turns out to be Bomba's. He is too absent-minded to notice his daughter standing right before him until she speaks to him. He is happy to see her, though we learn MK's mother passed away. Bomba also lives with his three-legged dog Ozzie. Bomba shows MK to her room, which is pink and girly.
Back in the forest, the Leafmen gather by a tree and are watched by other beings like mushrooms and flowers. Nod gets into an argument with Ronin, who reminds him he promised Nod's father he'd protect him after his passing. Nod decides to quit being a Leafman and leaves. Ronin goes to meet with Queen Tara (Beyonce Knowles), who has control over the nature of the forest. Ronin tries to come up with a plan to fight off the Boggans, but Tara has something else in mind that Ronin doesn't agree with. It's also hinted that the two have romantic feelings for each other. Tara also mentions that she must find an heir soon.
We move to Rotwood, a horribly decaying part of the forest. A Boggan general named Dagda (Blake Anderson) goes to meet with Mandrake (Christoph Waltz), his father and leader of the Boggans. They elaborate on their plan - to kill Queen Tara before she can find a successor so they can rot the forest.
A parade is happening with Tara and the Leafmen. One child known as Marigold Girl (Emma Kenney) is very fond of Tara and her powers over the forest. She asks her mother if she can be queen when she grows up, but she responds that it doesn't work that way.
Tara goes to Mub (Aziz Ansari) and Grub (Chris O'Dowd), a slug and snail, respectively, who are guarding pods that Tara will choose to bloom. Mub picks a large pod, but Tara notices a smaller one and chooses it. Suddenly, Ronin notices a rotting leaf, and the shoots an arrow at a tree. A Boggan falls, and the others emerge from the tree bark and attack. Ronin orders the Leafmen to protect Tara and the pod while he fights off the Boggans. Tara holds onto the pod as the Boggans take the other pods, and she rushes off. Marigold Girl helps Tara fight off the Boggans, for which she is grateful.
Meanwhile, Bomba is still set on finding more about the beings in the forest, but MK argues that he ought to put an end to this because it pushed everybody away, including MK and her mother. An alarm goes off, and Bomba rushes into the forest to respond. MK decides to pack her things and leave a note for her dad. She calls the cabbie to pick her up, but she gets no signal. That's when Ozzie runs out into the forest, forcing MK to chase after him.
Ronin grabs Tara on his bird, just as Mandrake and Dagda come in for the attack. Ronin shoots an arrow that kills Dagda, but Tara is hit by an arrow and she falls off the bird, still holding the pod. MK runs into the forest at that moment and sees Tara fall. She is stunned to see a small being. Tara literally breathes life into the pod, which floats up to MK. She grabs it, and it shrinks her down to the size of the others. Ronin and the other Leafmen come to Tara's side. She tells MK to bring the pod to Nim Galuu so that the pod can bloom in moonlight and the forest can prosper. Tara dies in Ronin's arms, and her body disappears into little particles. The pod has wrapped itself around MK's arm. Ronin tells a Leafman to go to a place called Moonhaven, and he takes MK on his bird. Mub and Grub arrive to join them.
Nod has taken up bird-racing in another area of the forest. After some competition, he wins, but is then taken by the gangster toad Bufo (Pitbull), who wanted Nod to lose. Ronin comes in to get Nod back and informs him of Tara's death. Nod meets MK, and they all head off to complete the mission.
The team rides to find a bunch of Boggan crows surrounding an area. MK and Nod run off and fall in a hole. Inside is a mouse who initially appears cute but turns out to be antagonistic. Nod tells MK to jump out of the hole, and she's surprised that she can jump so high, but she hits a branch and knocks herself out. Ronin comes in and scares the mouse away. When MK comes to, he tells Nod he has to ride with Mub and Grub, while MK goes with Ronin. Mub, who is smitten with MK, tells Nod to back off, though he is not intimidated.
Mandrake has a couple of Boggans force Bufo to meet with him. Bufo makes an insulting remark about Mandrake's son, which angers him enough to take down a whole tree. Mandrake threatens to kill Bufo unless he gives him the information he wants regarding the Leafmen.
The team makes it to a tree where many other forest beings are gathered. Before them all is Nim Galuu (Steven Tyler), a caterpillar who is also the scrollkeeper of the forest. He sings a song and is stunned when he reads about Tara's death. He finds Ronin and the others, and MK gives him the pod. Unfortunately, Nim doesn't know how to get the pod to bloom. He takes the team to find the scrolls that will determine how they can succeed. MK asks Nim how she can get home, and he opens a scroll that depicts MK's memory of when she encountered Tara. What she didn't hear was Tara saying that MK was brought there for a reason, and even though she can't see it, it is there, echoing something Bomba told her earlier.
Ronin tells Nod to look after the pod, but he takes MK outside and they spot a deer. MK is amazed and rides with Nod through the forest. Meanwhile, Mandrake crashes into the tree on a mole and kidnaps Mub and Grub, who know how to get the pod to bloom as they are also guarding it. Ronin finds Nod and chastises him and MK for their failure to secure the pod. They then come up with a plan to get it back.
Mandrake takes Mub and Grub back to Rotwood and tells them he plans on having the pod bloom in darkness so that he can have control over the forest. They tell him it doesn't say that in the scrolls, but he got the scroll for himself to prove them wrong.
At night, the trio go infiltrate Bomba's home. They find the professor walking around and identify him as a stomper, since he is always going around the forest looking for them. MK is upset when they make fun of him, and she goes to try and get his attention. Bomba, meanwhile, has already found MK's note and is hurt by what he's read. While Nod and Ronin grab animal skeletons that Bomba has, MK is spotted by Ozzie. She runs away from him, and Bomba notices her and the other two tiny people running. He grabs a vacuum and tries to suck them up, but only gets MK. He is stunned to find her to be two inches tall, and he faints, dropping the vacuum container and breaking it, allowing MK to be free. She gives her dad a kiss on the forehead and places a thumbtack on a map on his table, and then rejoins Nod and Ronin.
With the animal skeletons, the trio go into Rotwood. Ronin creates a distraction for the Boggans and has MK and Nod go find Mub and Grub. They grab them and the pod and escape while Ronin fights off the Boggans, just as Mandrake drops in. They duke it out, and Mandrake calls upon his army to attack. Ronin stays behind to fight them off, even telling Nod to go after Nod tries to save him. They take a hummingbird and fly off.
The four make it to Moonhaven, where Nim Galuu and the other beings are waiting. He places the pod in a spot where the moon will touch it. Suddenly, the moon is eclipsed by a horde of bats set upon by Mandrake. The Leafmen spring into action and fight off the Boggans, while MK is left by the pod. She then realizes she must get her dad to help. She takes a hummingbird and rushes to find him, but the pod starts to bloom in darkness.
MK tries to get Bomba's attention with the security cameras, but he feels dejected and believes he was imagining what he saw. He disconnects the cameras even as Ozzie tries to show him that MK is calling for him. He then spots the thumbtack on the map and runs out to find MK.
A Boggan chases MK, but Ozzie grabs it and takes it down. Bomba finds MK and communicates with her through his headgear (everything Bomba say and does sounds slow and distorted to the Leafmen, while they are fast and high-pitched for him). She leads her dad to Moonhaven and has him take out his iPod, which contains a frequency of bat noises, and uses the speakers to drive them out. The bats chase Bomba, but the moon is no longer eclipsed.
Mandrake comes down into Moonhaven to try and grab the pod, but Ronin shows up to fight him off. They fight again, but Mandrake almost kills him with his poison arrow. Nod shows up to defend Ronin, just when other Leafmen arrive. They hold Mandrake back long enough for the moonlight to hit the pod so it can bloom. The effect is powerful enough to push Mandrake away into the rotting of a tree, which absorbs him and traps him into the tree as it heals, just as the rest of the forest becomes beautiful again.
Tara's spirit comes from the pod and spots Marigold Girl. She grants her wish and picks her to be her successor. Tara also looks at Ronin, who is smiling again as she'd hoped. Nod then decides to rejoin the Leafmen, and Ronin makes Grub, who has been wanting to be a Leafman the whole time, into a warrior himself. Marigold Girl then uses her new powers to help MK grow back to normal, but not before she finally kisses Nod. Once she is back to normal, she reunites with Bomba, and they hug.
Sometime later, Bomba is drawing the Leafmen with MK's help. He suggests they ought to use acorns for helmets. A little alarm goes off, and Bomba uses his computers to have MK keep in touch with Nod. Mub shows up, still jealous of their relationship, and he apparently tries to swallow Nod. MK decides she should go help Nod out, and Bomba gives her her own headgear to help. MK gives him his own headgear, and the two set off back into the forest once again.
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