John Mala was a local Hawaiian boy headed for big time trouble until McGarrett, using his US Navy background, got Johnny to enlist in the USN. But Johnny could not cope with the structure and rules and went AWOL. He is spotted by USN Shore Patrol (SP`s the police for the Navy) and chased. In a struggle with one of the SPs at a ballpark, Johnny gets a hold of the SP`s 45 handgun and off camera a shot is heard, Johnny runs and the other SP, Walt Kramer (Christopher Walken) comes to the body of his fallen comrade laying dead.
The word gets out to Five-O since this happened on Hawaiian soil and he goes to visit Mrs. Mala to ask about her son. She distrusts everything she knows about the history of McGarrett and Johnny fearing for her son`s safety knowing the SP was killed. Young Tommy Mala, seeing this, remains silent as well.
Back at Five-O HQ, Steve is troubled by the incident, he does not think Johnny could be capable of shooting someone. Tommy sneaks into McGarrett`s office with a message from his mother, he is to take McGarrett to get Johnny in a sugar cane field. They bring in Johnny and McGarrett questions him, he does not remember firing the gun, but he remembers hearing the shot whistle past his ear. McGarrett introduces an attorney who tries to start putting together a defense for Johnny, but Johnny sees this as betrayal by McGarrett, he is stuck in the system and doomed for prison.
Back at Five-O HQ, McGarrett gets the whole team together and gives them assignments to investigate the shooting, including going over the entire crime scene at the ballpark to find the missing 45 slug. Chin and Kono are looking for the slug at the park, and try to recreate the angles that the lab has for the murder, a shot from above the head piercing through and deflecting out under the left shoulder. Each angle they try seems to have holes in the balistics path, until Chin goes high up a ramp and with a trash can moved, he and Kono see where the shot was from above and ricoched off the pavement into a wooden support beam--they have the badly deformed slug for McGarrett.
Meanwhile Johnny overpowers a prison guard and steals his sidearm escaping to a military area. The SP want to move in but McGarrett convinces them to let him try first to prevent unnecessary loss of life, armed Johnny`s and the SPs. Johnny and McGarrett meet and Johnny warns him off, even shooting at his feet, but Steve keeps coming. They fight all over the bluff top until McGarrett convinces Johnny to come in.
Back at Five-O HQ, McGarrett is concerned about the ballistics and the fatal wound for SP Waters. Using chalk and a crude drawing of the ballpark ramp with paper cutouts for Johnny and the SP Waters, he sees where it was impossible for a close range shot because there were NO gunpowder burns on Waters, thus the shot scientifically had to be from further away than Johnny could have fired with Waters 45 gun.
He follows Kramer with Water`s widow Sue to her apartment, and after watching an exchange where Kramer tries to sooth Sue, confronts Kramers alone. He asks to take a ride, and Kramer is suspicious but takes McGarrett to the ballpark. En route they discuss Sue and Kramer admits they were very close once, before the Navy, but then Sue fell in love with Waters and married him instead.
At the ballpark, McGarrett goes over the evidence with Kramer, discussing angles and the lack of powder burns, and even the connection Sue has with Kramer. He hints that maybe there was an accident that day of the shooting, that Johnny did not shoot Waters but Kramer did. Kramer points out his 45 was returned to the armory with a full clip, but that Waters gun was missing one shot. McGarrett proposes that Kramer switched clips when he was standing over his friend`s body to cover the evidence, and after some more interrogation Kramer admits he shot Waters from above when he saw the struggle trying to hit Johnny, but killing the SP instead.
The show ends with McGarrett bringing Johnny back to his family, and a smile as he watches the reunion.