Centuries ago, a devastating war threatened to tear the land apart. According to legend, a knight known as Sir Aaron, who wielded the mysterious power of Aura, stopped the conflict with the help of his trusted partner, a Pokémon named Lucario. The kingdom of Rota was saved, and Sir Aaron was forever celebrated as the Wave-Guiding Hero. However, before his final act, he mysteriously sealed Lucario within his staff, leaving the Pokémon confused and feeling abandoned for generations.

In the present day, Ash Ketchum and his friends Brock, May, and Max arrive in the town of Rota, where an annual festival is being held at Cameran Palace to honor Sir Aaron's legacy. Eager to participate, Ash enters a Pokémon tournament and, with Pikachu by his side, wins the competition. As the honorary Wave-Guiding Hero of the year, he is presented with Sir Aaron's ancient staff. During the celebratory ball that follows, the scene is interrupted by the sudden appearance of Mew, a rare and playful Legendary Pokémon. Startled by a pair of Weavile trying to capture it, Mew flees in a panic, accidentally taking Pikachu and the Team Rocket member Meowth with it toward a mysterious and dangerous location known as the Tree of the World's Beginning, also called the Tree of Beginnings.

As Ash reaches for the staff in shock, his own Aura, which is similar to Sir Aaron's, awakens Lucario from his centuries-long imprisonment. The Aura Pokémon emerges confused and bitter, initially mistaking Ash for his former master due to their similar Aura signatures. Distrustful of humans because he believes Sir Aaron abandoned both him and the kingdom, Lucario is reluctant to help. However, driven by his unwavering promise to never leave Pikachu behind, Ash convinces the skeptical Lucario to guide him to the Tree of Beginnings to rescue his partner. The group sets out on a perilous journey, soon discovering they are not alone. The tree is fiercely protected by three ancient golem Pokémon: Regirock, Regice, and Registeel, who attack any intruders on sight.

Upon reaching the Tree of Beginnings, a vast and organic ecosystem, the group becomes separated. Inside, Ash and Lucario uncover the truth of the past through Time Flowers, crystal-like objects that show glimpses of history. They learn that Sir Aaron did not betray Lucario or his kingdom. Instead, he made a heroic sacrifice, giving up his own life force to power the Tree of Beginnings and stop the war, sealing Lucario away only to prevent him from sharing the same fate. Realizing his master's true love and bravery, Lucario finds closure.

As the group attempts to rescue Pikachu from Mew, the tree's immune system activates, viewing the human intruders as threats. Ash, Brock, May, and Max are absorbed by the tree, leaving only their Pokémon behind. To save them, Lucario understands he must replicate Sir Aaron's sacrifice. He uses his own Aura to revive the dying tree and restore his friends. With a final, heartfelt farewell, Lucario succeeds, saving everyone but fading away himself. In the end, the group returns to Cameran Palace, and the kingdom finally recognizes Lucario as the true hero he always was, reunited with Sir Aaron in the afterlife.