Professor Sparks, a renowned scientist and inventor throughout the world, is leaving his home (The titular Mystery Mountain) for an important meeting. To supervise his michievous daughter Polly, Sparks assigns Botley, one of his robots, to do so.
One day, Polly came home exasperated over a history test result. Therefore, in order for her to pass the test, she uses her father's time machine to send 25 robots back in time in order to alter history, hence making her answers on the test correct. Botley, seeing this development happening, brings along the player to help him get all the robots back from their respective time periods to the mountain. In order for this to occur, however, the following must be done:
1. A specific robot will be designated for the rescue mission.
2. Polly would then hide four objects (called Mission Clues) all over the mountain. These objects hold the secret to the whereabouts of the robot.
3. These items and 1000 invention points are then collected. Both are attainable through playing some mini-educational games.
4. The Wheel of Invention is used to analyze these four Mission Clues to set up the time machine as to where the robot is.
5. Robot is brought back to mountain via a Recall button.
6. Repeat steps 1-5 until all the robots have returned.
After the robots are rescued, Polly then attempts to send Botley into the time machine and to the beginning of the universe, so the "Big Bang" will be replaced by the "Big Bot", hence killing Botley in the process. However, Professor Sparks had just returns to catch Polly in the act. For her tomfoolery Polly would need take a latin test, which Polly absolutely despises.