Joe 90 becomes a balloonist to rescue his kidnapped father.
Professor McClaine is kidnapped by members of an international espionage ring anxious to discover the secrets of a closely-guarded file marked "File 90." They are determined to learn more about the BIG RAT, and refuse to believe the Professor, when he volunteers the information that it stands for Brain Impulse Galvanoscope Record and Transfer, and that it transfers brain patterns to Mac's nine-year-old son, Joe. They refuse to take him seriously, especially when he says that Joe carries out dangerous missions for W.I.N., and prepare to torture him to extract what they hope will be the truth.
Mac is being held prisoner in a remote Alpine clinic, inaccessible except for a ski lift, operated from the clinic. Meanwhile, Shane Weston, Sam Loover and Joe are holiday-making in the Alps. Unbeknown to the kidnappers, details of Mac's plight are passed on to them, and Joe goes to his father's rescue in a balloon. It drifts slowly towards the clinic, but time is precious. It seems impossible for Joe to reach Mac in time to save him from his terrible torture, but with moments to spare Joe breaks through the glass sky-light in the clinic roof. Mac is saved, but the kidnappers still believe that they have won the day when they rush for the ski-lift and escape - only to find themselves face to face with Weston and Sam at the bottom.