Frank Murphy (Roy Scheider) is a "Metropolitan Police Department" air support division pilot and troubled Vietnam War veteran with post traumatic stress disorder (PTSD). His newly assigned observer is novice Richard Lymangood (Daniel Stern). The two patrol Los Angeles at night and give assistance to police forces on the ground.
Murphy is instructed to attend a sunrise demonstration in the Mojave Desert at "Pinkville", and is selected to pilot an advanced helicopter, informally called "The Special" and nicknamed "Blue Thunder", during an evaluation exercise. It is a military-style combat aircraft intended for police use in surveillance and against possible large-scale civic disobedience during the then-upcoming 1984 Olympic games. With powerful armament, and other accoutrements such as thermal infrared scanners, unidirectional microphones and cameras, built-in mobile telephone, computer and modem, and a U-Matic Video Cassette Recorder (VCR), Blue Thunder appears to be a formidable tool in the war on crime. Murphy notes wryly that with enough of these helicopters "you could run the whole damn country."
When the death of city councilwoman Diana McNeely turns out to be more than just a random murder, Murphy begins his own covert investigation. He discovers that a subversive action group is intending instead to use Blue Thunder in a military role to quell disorder under the project codename T.H.O.R. ("Tactical Helicopter Offensive Response"), and is secretly eliminating political opponents to advance its agenda.
Murphy suspects the involvement of his old wartime nemesis, former United States Army Colonel F.E. Cochrane (Malcolm McDowell), the primary test pilot for Blue Thunder and someone who felt Murphy was "unsuitable" for the program. Murphy and Lymangood use Blue Thunder to record a meeting between Cochrane and the other government officials which would implicate them in the conspiracy, but Cochrane looks outside and sees Blue Thunder and realizes what has happened. After landing, Lymangood secures the tape and hides it, but is captured upon returning to his home, interrogated, and then killed while trying to escape. Murphy hijacks Blue Thunder and arranges to have his girlfriend Kate (Candy Clark) retrieve the tape and deliver it to the local news station, using the helicopter to thwart her pursuers. Kate arrives at the news station, but is almost captured by one of the conspirators; the reporter Kate was sent to find intercepts Kate and gets the tape back, while the conspirator is knocked unconscious by a security guard.
Two Air National Guard F-16 fighters are deployed to deal with Murphy, but he manages to shoot one down and evade the other. However, in the process, one missile destroys a barbecue stand in Little Tokyo and a second impacts ARCO Plaza. The operation is then suspended by the mayor. Cochrane, disobeying orders to stand down, ambushes Blue Thunder in a heavily armed Hughes 500 helicopter, and after a tense battle, Murphy is able to shoot him down after executing a 360° loop through use of Blue Thunder's turbine boost function. Murphy then destroys Blue Thunder by landing it in front of an approaching freight train.
In the meantime, the tape is made public and, as a result, the conspirators are arrested.
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