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 immmediately 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-satisifed 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 unforuntely later on is killed just before she arrives at Chaney's house and mumbles the words ""K.G.B."".

The search turns into an evenmore vengeful one, but when revealing the location of the Sabre jet, Blue Thunder i