An undercover operation involving Lady Penelope and a Parker to recover a stolen Repulser Magnetic Array for the Global Defence Force gets blown prematurely. Parker is taken prisoner by Banino using the power of the Repulser and he takes a stolen GDF flyer with Kayo, who was secretly acting as back-up, in pursuit in Thunderbird Shadow. The flyer crash lands on a factory roof and International Rescue intervene with Scott in Thunderbird 1 rescuing one of the factory workers and Lady Penelope saving Parker. Kayo confronts Banino to find he knows her secret; she lets him escape knowing she will have to reveal the truth of her past.
A number of carefully staged disasters require the full attention of everyone at International Rescue. Kayo discovers that the Hood is behind these acts of terrorism and has actually infiltrated Tracy Island. To make matters worse, the Hood has rigged up explosive devices to bring down the Thunderbird craft - and now he reveals his shocking secret to the Tracy brothers.
A geological survey team gets trapped when a huge Earthbreaking vehicle causes them to fall into a narrow crevice. Scott, Virgil and Kayo take off in Thunderbird 1, Thunderbird 2, and Thunderbird Shadow after the Earthbreaker takes out the responding GDF fliers. The vehicle's controller, known only as The Mechanic, attacks and damages Thunderbird 2, leaving Virgil no choice but to make an emergency crash landing back on Tracy Island. Meanwhile, Lady Penelope and Parker visit the Hood in Parkmoor Scrubs prison to find out more about this mysterious new villain. In the end, Scott evacuates the survey team while Kayo takes on the Mechanic. They barely make it out when the villain sets his vehicle to self-destruct.
GDF Captain Ridley O'Bannon sends out a distress call during a routine inspection of the derelict generation ship known as EDEN (intended to travel the stars for hundreds of years). John and Alan answer the call. Together, the trio explores the ship and discovers leftover equipment known as Builder Bots. They also find two space "pirates" named Reece and Dobbs causing mischief. As the mystery comes to an end, the pirates accidentally reverse the bots' programming, causing them to tear EDEN apart. With the help of John's Mech Suit, they escape.
Thunderbird 3 is called out to Europa, a moon of Jupiter, when a pair of documentarians fall into an ice ocean, leading Alan to make first contact with an alien lifeform.
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