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Francis McNeil Murphy is a cop in Los Angeles working in the Astro Division, flying helicopters for air patrol, one of the best pilots on the force. He was a Vietnam veteran who fought for his country did a tour in a half. During the war, he served under his commanding officer, F. E. Cochrane. During a mission in Vietnam, a Viet Cong man they had prisoner was taken in one of the helicopters and F. E. Cochrane ordered him to throw the man out of the chopper and he refused, so another man in the unit threw the man out. F.E. Cochrane tried to court martial Frank Murphy, but since he caught some shrapnel during a battle could not and that is why Frank got out of the Army.
Years later, Frank has had some flashbacks of the Vietnam War, he has had some nightmares about the War and during one of his flights working in the Astro Division had an issue where he messed up during a flight. His captain, Jack Braddock, decided not to take Frank off the flight status. Frank has found a way to control it by timing himself with his wristwatch. In 1983, Frank gets a new partner, Richard Lymangood, who would get the nickname "JAFO". Frank's former partner, Montoya, went to the day shift. Frank Murphy and Richard Lymangood go on their first flight together. Frank asks why Lymangood put in for air support and Lymangood answers he wanted something different. They see a robbery in progress and Lymangood learns that air support is not all that different. During the flight, they discover what they thought was an abandoned Chevy, but it was not abandoned. A man in the car was staking out Diane McNeely, a city council woman for the city of Los Angeles living in Brentwood. Muphy takes Lymangood to see a woman posing in the window of their home. They get a call on the radio concerning Diana McNeely, who gets assaulted. When they get back to the area where the Chevy was, they discover it is gone. They see the perps at Diane McNeely's home and get shot at. Murphy starts having some flashbacks of the Vietnam War.
When Murphy and Lymangood get back, they get their butts chewed out by Captain Braddock about them peeping in on the window in Encino. Captain Braddock tells Murphy about the assault and Braddock says they are calling it a rape and Murphy doesn't believe it is so. Captain Braddock tells Murphy and Lymangood that they are grounded till this thing blows over, Baddock dismisses Lymangood and talks to Murphy telling him the review board that he up for psychiatic re-avaluation. Murphy leaves and drives off really quick out of the precinct parking lot and goes home and checks his messages on his phone and finds that it is his ex-girlfriend, Kate. Kate opens the door with the key with her son and they talk. Later on that night, Frank goes to Diane McNeely's home to do some investigating and finds a piece of paper with the word "THOR" on it. Frank Murphy gets a call from Captain Braddock and he tells Frank that he is back on flying status and tells him he and Lymangood are assigned to a special detail. Frank meets up with Captain Baddock with Icelan and Fletcher, members of the U.S. government. They tell Frank about a special helicopter on their way to a military test site called "Pinkville", The helicopter was given a name, "Blue Thunder". During the demonstration at Pinkville, Blue Thunder was being demonstrated on its flight and weapons capability.
After the test, they would meet the pilot, F.E. Cochrane, an old aquaintance of Frank Murphy during the Vietnam War. F.E. Cochrane is still in the military, now promoted to rank of Colonel. Cochrane is not too pleased that Murphy was selected to fly Blue Thunder. Cochrane and Murphy talk some and Cochrane say to Murphy that they could have used a helicopter like Blue Thunder during the Vietnam War. Cochrane started to be arrogant with Murphy and when Cochrane leaves, tells him "Catch you later!".
A couple of days later at the precinct, Frank Murphy visits Montoya and asks him about the piece of paper with the word "THOR" on it and Montoya tells him he will get back with him on it. Cochrane would take a test flight in Blue Thunder with Frank Murphy and Richard Lymangood in another helicopter. Before the flight, Cochrane had a conversation about the impossibility of looping a chopper, which Frank Murphy told Lymangood he did once. Cochrane sabotages Murphy's chopper's turbine and before the flight, he tells Murphy to follow my leader and says to Murphy "Catch you later!". During the flight, Murphy's chopper ended up losing control and he and Lymangood nearly crashed but managed to save themselves by landing on a construction site on the foreman's trailer. Later on that night, Cochrane runs into Frank Murphy as Murphy is getting ready to leave, he gives Murphy a hard time about the flight and tells Cochrane to "back off" and Cochrane thinks Murphy is threatening him, but just tells him to "back off" and before Cochrane leaves, he says "Catch you later!".
Later on that week, Murphy and Lymangood take Blue Thunder for a test flight that night and after they were called to return to base, Murphy sees Cochrane driving off in a hurry with Fletcher and decided to follow them and they go to the Federal Building. Murphy and Lymangood overhear the conversation with Blue Thunder's technology and hear that they are responsible for city councilwoman Diane McNeely's death and hear Cochrane planning on taking out Murphy himself. Cochrane walks over to the window and pulls the curtains and sees Blue Thunder and they speed away from the building. Later on that night, Lymangood hides the tape of the conversation and is murdered by one of the government men named Grundelius and Murphy is framed for the murder. Frank is out driving that night and goes to Lymangood's home and sees that his partner is murdered. Frank overhears on the police radio that he is wanted for questioning and drives off. Frank calls his home phone and checks his messages, one of them from Kate, who heard about Lymangood and a message from Lymangood telling him that there is a message in Blue Thunder on where the tape is hidden.
The next day at the precinct, Cochrane, along with Icelan are trying to find away to erase the tape, but can't since Lymangood changed the code. Frank Murphy manages to sneak into the precinct and gets the message Lymangood left for him where he hid the tape and Lymangood found out what JAFO stands for, "Just Another Fucking Observer". Murphy steals Blue Thunder and takes off in the helicopter. Cochrane sees Murphy taking off in Blue Thunder and tries to shoot Murphy, but is too far away. While at the tower, Cochrane and Icelan overhear the conversation of Murphy contacting his former girlfriend Kate talking about the tape hidden at the Drive-In in a dumpster behind the concession stand and plans to have her take it to KLAB TV, one of the big TV stations in L.A. and send Fletcher to intercept her, but Fletcher fails and Kate and reporter Alf Hewitt go to the studio upstairs and watch the tape and learn the truth about Blue Thunder. After the failed attempts to bring Murphy down by the L.A.P.D. and the Air Force, the mayor calls off the hunt. Cochrane decides to go after Murphy, though he was ordered to stand down. Cochrane took off in a helicopter with heavy artillery.
A battle of the skies went on with Cochrane and Murphy, Cochrane managed to wound Murphy some and cause a malfunction with Blue Thunder's weapons, but later on Murphy manages to to get the upper hand and makes Cochrane play "Follow the leader" and Murphy manages to do a loop in Blue Thunder and Cochrane could not believe that Murphy is doing it and decides to try the loop to follow Murphy, but with the turbo mode, Murphy makes the full loop and shoots Cochrane's chopper, killing him. After Cochrane dies, Murphy says to the dead Cochrane "Catch you later!". Frank Murphy lands Blue Thunder in front of a freight train, destroying Blue Thunder.