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The Space Shuttle Argo, privately funded and arranged without any governmental interference, becomes under threat by a group of weapon dealers who don't want their sales of bacterial weapons falling down heavily because of this. This is because, the shuttle has successfully performed an gene-splicing experiment in outer space, relieving the American Space Industry after it is set for the shuttle to re-enter orbit, but there is one slight problem.

The experimental canister has to be transported from the moment the shuttle touches down, to an unknown designated laboratory, where it will be configured and analysed to affect the usage of bacterial weaponry, in 20 minutes. Only Blue Thunder has the speed capabilities to achieve this, and so Apex lends the unit to them.

After a accident involving the helicopter's entire electronics being short-circuited by power lines at a nearby power plant where the team managed to apprehend two men linked to the trading of German Warfare products, Professor Von Hartig, the man responsible for designing the sophisticated electronic systems of Blue Thunder, is contacted to introduce an electronic countermeasures shield system to the aircraft.

Two security key-cards are handed out, one for Chaney, the other for Von Hartig, but when the group of dealers psychologically brainwash the Professor, he accomplishes in destroying both cards, leaving Blue Thunder totally defenceless against the group's modified Huey chopper, armed with a laser cannon, which is intended to destroy the Argo Shuttle, and Blue Thunder, if it lies in it's path.