In this Junior Adventure, Putt-Putt must travel through time to rescue his dog Pep and retrieve his lunchbox, calculator, and history report. This was the first Putt-Putt game to have multiple paths — the missing objects could be in one of four locations, meaning there could be different puzzles on different playthroughs.

Putt-Putt drops by Mr. Firebird's lab before school to show him his history report, lunchbox, and calculator. There, he is amazed to discover that Mr. Firebird has invented a time machine — and horrified when an accident sucks his school supplies, and his dog Pep, into the machine, scattering them through time and space. Putt-Putt must therefore use the time machine and travel to four periods — the age of the dinosaurs, the Middle Ages, the Wild West, and the far future — to retrieve them.