The series takes place in 2086 and chronicles the adventures of a rescue team called the "Thunderbirds" ("TechnoBoyager" in the Japanese version, a portmanteau of "technology" and "voyager" with the last part coming out as "boyager" due to V's and B's being switched around in the Japanese language),[needs independent confirmation] who work for the International Rescue Organization (IRO).

Although the English version is called Thunderbirds 2086, the Tracy family, who ran International Rescue in the original series, is not mentioned.

The animated series otherwise has notable similarities to the original, with most episodes revolving around a natural or man-made disaster that the Thunderbirds team must investigate and help resolve.

Unlike the original series, Thunderbirds 2086 also has an ongoing story arc revolving around a breakaway independence group known as the Shadow Axis, led by the mysterious Star Crusher.

He has a nephew, Skipper Simpson (named Paul in the Japanese version), a young boy who idolizes the Thunderbirds and hopes to one day join their ranks.

Oddly, the introductory dialogue in the English version describes the characters as cadets, while all of the episodes rank them as captains.