The Templeton brothers, Tim and Ted, have grown apart over the years, leading starkly different lives. Tim is now a married stay-at-home dad, raising two daughters, while Ted has become a successful CEO. Despite their achievements, there's an underlying disconnect, with Tim nostalgic for their childhood adventures and Ted immersed in his corporate lifestyle. However, the unexpected reappearance of a new Boss Baby, Tina – Tim's youngest daughter, who's a top-secret agent for BabyCorp – brings the brothers back into each other's orbits. Tina reveals a new mission that requires their help to thwart an evil plan, compelling the brothers to revisit their past.

The mission hinges on getting into a prestigious school known for its innovative educational methods, run by the enigmatic founder Dr. Erwin Armstrong. Ted and Tim must undercover as children again, thanks to a special formula that temporarily turns them back into their younger selves. Their transformation is not just physical but also serves as a catalyst for the brothers to address their unresolved issues and to bond once again. Inside the school, they navigate its educational wonders and pitfalls while attempting to uncover the dastardly plot that threatens to disrupt the balance between babies and adults. Their adventure is a wild mishmash of sibling rivalry, action-packed escapades, and heartfelt moments that underscore the importance of family and childhood.