The New World Aircraft Corporation gives Brains an open invitation to design a new aircraft. When he suggests an airship, he is mocked and ridiculed, although the NWAC go ahead and build the antigravity Skyship One. While Alan, Tin Tin, Lady Penelope and Parker travel on the Skyship's maiden voyage as International Rescue's represenatives, Brains remains on Tracy Island, designing Thunderbird 6. Each of his designs is dismissed by Jeff Tracy.
Unbeknownst to International Rescue, however, a man known only as the Black Phantom is moving against them. Tired of merely taking photographs, he plans to hijack the Thunderbirds themselves. His agents murder and replace the crew of the airship, and plant recording devices around Lady Penelope. Their plan is to Quote Mine her to summon the Thunderbirds to the Black Phantom's remote base, where he will be able to steal those magnificent machines. Unfortunately for the villains, Alan works out their plan, and Lady Penelope is able to warn International Rescue just in time. Thunderbirds 1 and 2 destroy the Black Phantom's base. On the airship, however, things aren't going so smoothly. A gunfight disables the ship's antigravity system, and it plunges towards a British missile base. All the Thunderbird craft are too heavy to attempt a rescue - except the antique Tiger Moth biplane that Alan and Tin Tin had flown to meet the airship. Brains flies the Moth onto the top of the airship, scooping his friends clear in the nick of time. Despite battle damage, Brains is able to land the plane safely. The Tiger Moth is then declared the new Thunderbird 6.
- Bad Boss: Imposter!Foster has no qualms about betraying his underlings if it benefits him.
- Bluff the Eavesdropper: When Lady Penelope is talking with Alan about Skyship One's captain Foster, of whom they both already suspect that he is not who he claims to be, the lamp next to her bed falls of the table, revealing a listening device underneath. Realizing the ship's crew is eavesdropping on her, she quickly alters her opinion about Foster and tells Alan they shouldn't jump to conclusions so fast.
- Break Out the Museum Piece:Chekhov's Armoury: When all their usual vehicles are unable to reach the stranded Skyship One, an old-fashioned biplane (that Alan used earlier to travel to England) is used instead. Imposter!Foster lampshades this by stating they (International Rescue) must have gotten it straight out of a museum.
- Broken Aesop: Jeff repeatedly turns down Brains' ideas for a new Thunderbird on the basis that the ideas are only suitable for a single type of rescue mission. Fine and good, except that (a) this applies to every single one of TB2's pod vehicles including Thunderbird 4, all of which Jeff presumably approves of, and (b) it's hard to conceive of any great number of uses for the vehicle that ultimately is made Thunderbird 6. In fact, it's not clear why Jeff thinks they need a Thunderbird 6...
- The Charmer: Imposter!Foster. One of the reasons Alan doesn't trust him.
- Continuity Nod: The Ski Thrusters from The Cham-Cham, which enable the characters to ski uphill, make another appearance.
- Cool Ship
- Thunderbird 6 is an antique Tiger Moth biplane. It earned the name when it proved the only aircraft in the Tracy arsenal both light enough and slow enough to land on top of a distressed luxury zeppelin.
- Brains also designed several Thunderbird 6 prototypes more in-line with the original five units — each was a perfectly viable vehicle in their own right, but all were rejected because Brains was going through a Heroic BSoD at the moment.
- Circle of Shame: When Brains outlines his idea of building an airship, a roomful of air industry executives laugh at him. The film's DVD Commentary points out that, since all the characters are marionettes, lots of laughing puppet heads had to be constructed even though each of them would only appear in one shot."Sure, they laughed — and then they built it!"
- Darker and Edgier: Not only is the original crew of Skyship One brutally murdered, we actually see their corpses being tossed into the ocean.
- Also, according to Word of God, the Black Phantom is actually killed when Thunderbirds 1 and 2 destroy his base.
- Dragon with an Agenda: Imposter!Foster. He continues to be The Heavy long after Big Bad The Black Phantom has been killed.
- Dropped a Bridge on Him: The Black Phantom.
- Expy: The Black Phantom for the Hood... maybe. Confusingly, he is the Hood - as in, literally the same puppet with a wig on - but the film implies he isn't, and Word of God is that he's not. (Sylvia Anderson called him "Hood Jr", which is either acknowledging he's an Expy or literally means he's an unknown family member.)
- Faux Affably Evil: Imposter!Foster is perfectly personable and a very convincing airhost, joining his guests for dinner on several occasions. His charm gradually fades when his cover is blown, though.
- Quote Mine: The Black Phantom's agents use recordings of Lady Penelope's voice to construct a new message they want her to say, and broadcast it to International Rescue.
- She Is Not My Girlfriend: Somewhat surprisingly, Alan and Tin Tin deny to Imposter!Foster that they are in a relationship, as it would distract from their duties. Apparently, Alan has outgrown his Crazy Jealous Guy tendencies.