The Templeton brothers have become adults and drifted away from each other, but a new boss baby with a cutting-edge approach is about to bring them together again - and inspire a new family business.
- Set 30 years after the events of the first film, Tim Templeton is now fully grown and lives with his wife Carol and their two daughters, Tabitha and Tina. Tim's younger brother Ted is now a successful CEO and is never around, instead sending lavish gifts to Tim and his family.
Tabitha is exhibiting more grown-up behavior, and one night while a discouraged Tim wonders about the person his daughter is becoming, he hears something coming from infant daughter Tina's room. When he goes to investigate, he discovers that Tina is a Boss Baby, just as Ted once was, and that she has been assigned to get Ted there for a special mission. Tim refuses to call, saying that he will never come, and encourages Tina to go back to sleep. However, Tina leaves a false voicemail for Ted, inviting him to come.
Tim wakes up the next morning to find a concerned Ted at his front door. Ted, Tim, and Tina all go into the kitchen, where Tim tries to explain that Tina is a Boss Baby and Ted just doesn't remember that he was one, too. As they start to argue, Tina reveals herself as a Boss Baby and gives them both magic pacifiers. Tina introduces the brothers to a new formula that BabyCorp has developed that will allow them to turn back into kids for 48 hours so they can infiltrate Tabitha's school undercover and figure out what Dr. Erwin Armstrong, founder and principal of the school, is planning behind parents' back.
The next morning, Tim follows Tabitha to her class and Ted is placed with all of the other babies. Ted rallies the other babies to help him get out of the playroom so that he can meet Tim in Armstrong's office, while Tim tries to get sent to the principal's office by disrupting class, but is instead put in "The Box" for timeout. Ted discovers that Dr. Armstrong is actually himself a baby, having run away from home after realizing that he was smarter than his parents, and reveals that B-Day is coming, which will get rid of parents so that they can not tell their children what to do anymore. After being unable to get ahold of BabyCorp and seeing that the brothers are once again drifting apart, Tina makes a show of quitting and says that they will complete the mission themselves.
On the night of the holiday pageant, Ted hangs out with Armstrong in the VIP section, where it is revealed that B-Day is set to happen that night through his new app, QT-Snap, which will send out a hypnotic signal to turn the parents into zombies. Both Tim and Ted are caught by Armstrong's ninja babies and are put in The Box, which slowly starts to fill with water.
Tabitha is able to sing her solo beautifully, while the brothers reconcile after it seems they are doomed. When Tabitha is done and she sees that Tim is not there, and no one in the audience moves due to being hypnotized, she runs off the stage crying. She is consoled by Tina, who reveals her identity as a Boss Baby, and she agrees to help her sister by getting to the server and shutting down QT-Snap before it can go worldwide. Ted is able to call Precious, Tabitha's pet pony, into the school, who breaks them out of The Box. The brothers are confronted by the ninja babies, but they are able to get away with the help of Ted's new baby friends.
Tim and Ted reach the server first, but they are stopped by Armstrong, who calls the zombie parents for backup. While the brothers fend them off, Tina and Tabitha get up to the server. Tabitha is able to hack in and pull up the shutdown screen, but the keyboard is destroyed by Armstrong. The sisters then set off a candy volcano using Mentos and soda, destroying the servers.
Tina reveals that her true mission was bringing Tim and Ted back together, and the brothers celebrate Christmas together as a family, while Armstrong returns to his own family.