Ted and Emily become suspicious of Beethoven's disappearances and follow him when he leaves their house one day and discover the puppies. Regina also finds the puppies and wants to drown them before she realizes they are worth money. Ted and Emily sneak the puppies out and hide them in the basement of their house. With the help of their sister, Ryce, the three kids alternate around the clock to bottle feed the four puppies. Their parents eventually find out and the kids convince them to let the puppies stay until they are old enough to go to new homes.
The Newton's are offered a free stay at a lake house belonging to one of his associates. Beethoven and his puppies accompany the family on their trip. The family and the dogs go to the county fair where George and Beethoven take part, and win, a burger eating contest. Beethoven wanders off from his family to discover Missy in a parked car. He helps get her free and the two go off. Around the same time, Regina finds Ted and Emily with the puppies and takes them. The kids find their parents and Ryce and the family goes off after them. After some persuasion they get the puppies back and Missy ends up back with Brillo in the end.