Seventeen-year-old Mary Katherine, also known as M.K., (Amanda Seyfried) relocates to live with her quirky scientist father, Professor Bomba (portrayed by Jason Sudeikis). He has dedicated his life to searching for tiny human warriors called Leafmen, who strive to safeguard the forest from malevolent creatures known as Boggans and their sinister leader, Mandrake (Christoph Waltz). Among the Leafmen is an independent and rebellious soldier named Nod (Josh Hutcherson), who decides to leave the group, much to the frustration of the strict Leafmen leader, Ronin (Colin Farrell). Nod, once Ronin's protégé and top soldier, struggles to adhere to orders and authority.
As the queen of the forest, Queen Tara (Beyoncé Knowles), contemplates her future, she must select an heir during an important ceremony. However, she is warned by Ronin about the Boggans diligently watching for an opportunity to thwart this selection. Despite the warnings, Tara is determined to proceed with a public affair, surrounded by her loyal protectors, including a laid-back slug named Mub (Aziz Ansari) and a hopeful snail named Grub (Chris O'Dowd).
With dark forces intent on wreaking havoc, the Boggans aim to eliminate Tara before she can choose her successor, threatening to throw the forest into chaos. Tara bravely selects the smallest pod as the heir. Just after her choice, the Boggans launch an assault, leading to a chaotic confrontation. Tara escapes, but not without difficulty, as her loyal guards are soon overtaken by the overwhelming number of foes. Using her powers, she manages to hold off her pursuers momentarily, aided by a flower child who reveres her. Ultimately, Ronin arrives to rescue her, and they flee together on Ronin's hummingbird steed. Tragically, during their escape, Mandrake and his son Dagda (Blake Anderson) attack, resulting in Dagda’s death at the hands of Ronin, while Tara suffers a fatal wound from Mandrake's arrow.
Meanwhile, feeling frustrated with her father's obsession, M.K. leaves a note and attempts to leave but is swiftly interrupted by her family's quirky dog, Ozzy, who dashes into the woods. Searching for Ozzy leads M.K. to witness Tara's fall, where she is entrusted with the heir pod before Tara succumbs. Tara implores M.K. to deliver the pod to a Glowworm named Nim Galuu (Steven Tyler) before fading away. M.K., confused yet afraid, teams up with Ronin, Mub, and Grub.
The adventure continues as Nod enters a race against various creatures, only to regret his decision when he finds himself in a dangerous situation with a tough bullfrog named Bufo (Pitbull). Ronin steps in to defend him, and eventually, Nod decides to join Ronin, M.K., Mub, and Grub upon hearing of the queen's death.
Their journey brings them to Nim Galuu, where M.K. unveils Tara's final message before being returned to her original size. During this escapade, romance blossoms between M.K. and Nod while the shadows of betrayal loom as Mandrake captures Mub and Grub, along with the precious pod, aiming to exploit it for his dark ambitions.
To infiltrate Boggan territory undetected, M.K., Nod, and Ronin embark on a mission to Bomba's house to secure disguises. M.K. learns that her father is viewed as a "stomper" by the Leafmen, while a mistaken encounter leads Bomba to discover that his theories may have been correct all along. Their journey culminates in an epic showdown, where Ronin and Nod realize the power of teamwork as they face Mandrake.
As the looming threat draws near, hope surfaces when moonlight overcomes Mandrake's darkness, causing the heir to blossom in light. The chosen heir, a marigold child who revered Tara, emerges, while Grub ascends to a Leafman. Reconciliations unfold, including a tender kiss between Nod and M.K., who then returns to her original size. After a heartfelt reunion with Bomba, M.K. joins him as an assistant, ensuring that the family maintains contact with their newly found small allies as they explore the wonders of their extraordinary world.
