When McGregor's nephew, Thomas, moves into the family manor, he is annoyed to find Peter Rabbit and his sisters in his garden. Thomas hatches plot after plot to get rid of them.

Bea, Thomas and the rabbits have created a makeshift family, but despite his best efforts, Peter can't seem to shake his mischievous reputation. Venturing out of the garden, Peter finds himself in a world where his mischief is appreciated. However, when his family risks everything to come looking for him, Peter must figure out what kind of bunny he wants to be.