Count Gruemon, a notorious swine, hated mice with a passion. One day, he discovered a mouse in his castle. Frustrated and irate, Count Gruemon ordered Puss 'N Boots (Pero) to find and destroy the mouse. However, Pero was a kind-hearted cat and had become friends with the mouse, and so, helped the little creature to escape. In a fit of anger, Count Gruemon, aided by Dr. Gari-gari, a fiendish scientist wolf, sent Pero on a perilous time-travel journey around the world and into the past.
Pero must locate and defeat Count Gruemon and the mad Dr. Gari-gari, and use their time machine to get home - or be stuck in the past forever. To make matters worse, the Cat Kingdom has sent Killers after Pero because he helped a mouse and thereby violated Cat Kingdom Law. Pero must travel to exotic lands and overcome many hazards, but can he defeat the combined might of the diabolical Count Gruemon, Dr. Gari-gari, and the Killers?