Years before meeting Shrek and Donkey, the adorable but tricky Puss in Boots must clear his name from all charges making him a wanted fugitive. While trying to steal magic beans from the infamous criminals Jack and Jill, the hero crosses paths with his female match, Kitty Softpaws, who leads Puss to his old friend, but now enemy, Humpty Dumpty. Memories of friendship and betrayal enlarges Puss’ doubt, but he eventually agrees to help the egg get the magic beans. Together, the three plan to steal the beans, get to the Giant’s castle, nab the golden goose, and clear Puss’ name.

The film revolves around a special team of trained secret agent animals, equipped with advanced tools that allow the mammalian members to talk to humans. The primary field team consists of guinea pigs Darwin, Blaster, and Juarez, star-nosed mole Speckles (cyber intelligence), and housefly Mooch (Reconnaissance). The unit’s leader Ben, orders an unauthorized infiltration of the residence of home electronics and appliances magnate, Leonard Saber, the owner of Saberling Industries, who has been under FBI investigation and is working for an unseen mastermind named Mr. Yanshu. The team is able to retrieve sensitive information about a sinister scheme that is set to occur in 48 hours. However, when Ben’s superior Kip Killian arrives for his evaluation, his astonishment at the team’s capabilities and technology is overcome by his indignation at Ben’s unauthorized mission and the fact that the downloaded intelligence appears to be useless information about Saber’s coffeemakers. As a result, the government agent orders the unit shut down, the equipment seized and the animals to be used as experimental subjects to be killed. With the help of their human compatriots, Darwin, Juarez, Blaster, Mooch and Speckles escape with hopes of stopping Saber’s scheme, but find themselves in a pet carrying case bound for a pet shop.