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The series follows Joe McClaine, a 9-year-old British schoolboy, the adopted son of Professor Ian "Mac" McClaine, a renowned computer expert. Residing in a secret underground laboratory is Mac's latest invention, the "BIG RAT" (Brain Impulse Galvanoscope Record and Transfer), a machine capable of recording knowledge and experience from leading experts in various fields and transferring it to another human brain. The central aspect of the design is the "Rat Trap", a rotating spherical cage in which a subject is seated during the transfer of the expert "brain pattern".
Sam Loover, a secret agent for the World Intelligence Network, persuades Mac, his friend, to dedicate the BIG RAT to WIN's pursuit of world peace by permitting Joe to assume such knowledge and experience and become a WIN agent. After the requisite skill is transferred, and provided that Joe is wearing special spectacles containing hidden electrodes storing the expertise, he is able to execute such missions as operating fighter aircraft, blasting off into space and performing advanced neurosurgery, all the while appearing to be an innocent schoolboy to the enemies of WIN. Since no one would usually suspect a child of espionage, Joe is WIN's "Most Special Agent". Reporting to the commander-in-chief of WIN's London Headquarters, Shane Weston, he is also provided with a special briefcase, which on superficial inspection appears to be a simple school case but in fact conceals an adapted handgun and WIN transceiver.
In a manner similar to other Gerry Anderson series, Joe 90 features gadgets, rescue operations, secret organisations, and criminal and terrorist threats to the safety of the world. A recurring foe for WIN is the "Eastern Alliance", which dominates Asia.
Joe 90 provides examples of:
- Clip Show: "The Birthday".
- Fun with Acronyms
- Hair of Gold: Joe.
- Kid Hero: The main character, Joe McClaine.
- Rescue: Some of Joe’s missions involve rescues.
- Sesquipedalian Loquaciousness: The title sequence proclaimed it to be filmed "In Videcolor" and "Supermarionation". Plain English translation: "It's in colour, and it's a (sophisticated) puppet show."
- Techno Wizard: Professor Ian McClaine.
- Teen Superspy: Pre-teen superspy actually, as Joe is only 9.
- Twenty Minutes Into the Future: The series was set in a future era (counting from the 1960s), probably 2012-13.
- Wake Up, Go to School, Save the World: Again, Joe McClaine.
- Wise Beyond Their Years: Justified: Joe uses the BIG RAT to instantly gain whatever knowledge or skills he needs for a mission, and only keeps this knowledge/skills for a single episde. Without the BIG RAT, he isn’t much smarter than an average nine-year-old.