While hosting a lively celebration in the charming town of Del Mar, Puss in Boots bravely confronts a gigantic foe, only to be struck down by a church bell. Following his recovery, the town's doctor, alarmed by Puss's reckless lifestyle, advises him to retire since he has already exhausted eight of his nine lives. Initially resistant to the idea, Puss ultimately yields to the doctor's wisdom after being injured in a duel with a menacing wolf at a local tavern. Deeply shaken by the encounter, he takes to the home of Mama Luna, an elderly cat lady, where he buries his tattered clothes. Months later, Puss finds companionship in a cheerful Chihuahua disguised as a cat, whom he affectionately names Perrito.
However, their tranquility shatters when the notorious crime family, led by Goldilocks and the Three Bears, arrives at Luna's home seeking Puss's expertise in stealing a coveted map that reveals the location of the elusive Wishing Star. Discovering what they believe to be Puss's grave, they leave, prompting Puss to pursue the Star in hopes of reclaiming his lost lives.
Puss and Perrito venture to the hidden lair of the nefarious pastry salesman and magical collector, Jack Horner, who plans to harness the Star's power to dominate the world's magic. During their attempt to steal the map from Horner, Puss encounters his vengeful ex-fiancée, Kitty Softpaws, who has her own motives for obtaining the map. As Goldi, the Bears, and Horner pursue them, Puss catches a glimpse of the wolf in the distance. Their journey leads them into the mysterious Dark Forest, a realm where travelers confront illusions born from their memories. As they face off, Puss is overtaken by a panic attack upon seeing the wolf's return, allowing Goldi to seize the map from Kitty.
After a heartwarming reunion with Perrito, who helps him regain his composure, Puss confides in him, sharing his fears and regrets about leaving Kitty before their wedding. He discovers that Kitty also chose not to attend, feeling that he was too self-absorbed to truly love her. With renewed determination, Puss and Kitty retrieve the map while Goldi and the Bears are momentarily distracted by a vision of their quaint woodland cottage. However, their escape leads Puss into a crystalline cave where spectral reflections of his past lives mock him for his change in perspective. The wolf reappears, revealing his identity as Death, who, incensed by Puss's disregard for his lives, intends to take his final life. Frightened, Puss dashes from the cave seeking the Star, abandoning Kitty and Perrito.
During a heated debate with the Bears, Goldi inadvertently discloses her wish to have a human family, leaving the Bears feeling disheartened yet willing to support her. Upon reaching the Star, Puss begins to voice his wish until Kitty intervenes, chastising him for his self-serving desire and expressing her own longing for trust. A skirmish ensues for possession of the map as Goldi briefly claims it, only to relinquish it to save Baby Bear, while Kitty traps Horner within his enchanted, bottomless bag.
In a dramatic twist, Death confronts Puss in a duel. Having learned the profound value of life through his experiences with his friends, Puss refrains from wishing for extra lives and instead accepts the challenge, managing to temporarily disarm Death. He boldly asserts that while he may never best him, he will tirelessly fight to preserve his last life. Recognizing Puss's newfound humility, Death begrudgingly spares him, knowing that their paths are destined to cross once more.
Meanwhile, Horner escapes his fate by consuming a magical treat, which transforms him into a gigantic version of himself. Perrito cleverly distracts him, allowing Puss, Kitty, and Goldi to destroy the map, triggering the Star to collapse and consume Horner before it bursts into the sky in a brilliant explosion. In the aftermath, Goldi assures the Bears that they are her true family, and they collectively decide to take over Horner's operation while Puss reignites his romance with Kitty. In the end, Puss, Kitty, and Perrito embark on an adventurous journey, stealing a ship and setting sail toward the Kingdom of Far Far Away, eager to reunite with old friends.
