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An F-86 Sabre jet is stolen from an airfield by a group of KGB mercenaries, followed by an intense but unsuccessful chase by security personnel. The subsequent day, FBI agent Bruce Walsh informs Captain Braddock, Chaney and the Blue Thunder crew to participate immediately in an in-depth search for the lost jet fighter, which with the proper treatment could be converted into a lethal weapon which could not be recovered by the government.

Chaney is dis-satisfied with Walsh not providing substantial information regarding the hi-jack but Walsh covers his own with the excuse of Apex having their full acceptance with the FBI on this case. Throughtout the assignment, Chaney soon starts to develop a very romantic and cosy relationship with Walsh's assistant, Kate Cunningham, who unfortunately later on is killed just before she arrives at Chaney's house and mumbles the words "K.G.B.".

The search turns into an even more vengeful one, but when revealing the location of the Sabre jet, Blue Thunder is shot down by heavy gunfire, and when repaired, Chaney and his men return to discover that Walsh is in fact the leader of this mercenary group whom intend in staging an attack on a Russian jet airliner and visualise it as a deliberate act from the United States Government, which would no doubt turn political matters into a globally-embarrassing frenzy.