Plot summary

At the Presidio U.S. Army base in San Francisco, MP Patti Jean Lynch (Jenette Goldstein) is shot dead while investigating a break-in on the base and two San Francisco Police officers are killed as they chase the thieves through the hilly streets of San Francisco and their car crashes on a street downtown. Jay Austin (Mark Harmon), a San Francisco police inspector, is sent to investigate. He clashes with Lieutenant Colonel Alan Caldwell (Sean Connery), the base Provost Marshal.Years ago, Austin and Lynch were partners while serving as MPs at the Presidio and Caldwell was their commanding officer. When Austin arrested Colonel Paul Lawrence (Dana Gladstone), Caldwell didn't support him. In the aftermath, Austin was demoted and decided to leave the army. Austin and Caldwell share a mutual dislike for one another.The murder investigation casts suspicion on Lawrence, as Lynch was killed with a Tokarev, a Russian pistol. Lawrence is the registered owner of a Tokarev, but claims he lost it in a poker game. Austin also learns that the getaway car used by Lynch's killer was registered to a civilian named Arthur Peale (Mark Blum), who is wealthy and owns a holding company that, in turn, owns other companies.Austin tries to question Lawrence about the Tokarev, but Caldwell intervenes. Austin's suspicions are further fueled that Caldwell will do anything to protect a fellow officer from civilian authorities, even if he is a killer. Recognizing that part of the case is under Caldwell's jurisdiction at the Presidio and part is under Austin's jurisdiction in San Francisco, they uneasily team up to investigate the case. Caldwell states that if the Tokarev bullet that killed Lynch were to match a bullet fired earlier from Lawrence's Tokarev at the Presidio firing range, then Caldwell will arrange for Lawrence to surrender to Austin for arrest.In the meantime, Caldwell and Austin visit Peale, who claims his car was simply stolen and has an alibi for the night Lynch was shot. However, Caldwell notices Vietnam-era paraphernalia in Peale's office. Using his own contacts, Caldwell learns that Peale was previously in the CIA, and a spy and military advisor in Vietnam at the same time Lawrence was there as an officer. It becomes clear that Lawrence and Peale knew each other.Austin gets the ballistics report back on the Tokarev, which confirms that Lawrence's gun killed Lynch. Ignoring his agreement with Caldwell, Austin corners Lawrence when he leaves the Presidio, resulting in a lengthy footchase through San Francisco's Chinatown. Ultimately, Lawrence is killed in a hit and run by someone driving a blue-colored Pontiac Trans-Am. Caldwell meets him at the scene and is furious that Austin disregarded their agreement.Compounding their past tension, Caldwell is also upset that Austin has started a relationship with his daughter Donna (Meg Ryan). Their relationship is rocky, with Donna alternately teasing and pushing Austin away. Caldwell confides in his friend, retired Sergeant Major Ross Maclure (Jack Warden), who runs the Presidio's war museum. It is revealed in backstory that Caldwell was Maclure's lieutenant during the Vietnam War. Caldwell was very green and relied heavily on Maclure. In one sequence, we learn that Maclure saved an injured Caldwell and attacked a Vietcong platoon waiting to ambush American soldiers, for which he was awarded the Medal of Honor.Caldwell and Austin both figure out that the killer at the Presidio was trying to break into a storeroom to retrieve a bottle of spring water that was delivered earlier that day. Following that lead to the company which delivered the water, Austin gets the name of the driver who made the delivery, George Spota (James Hooks Reynolds). Caldwell recognizes the name as someone who served under Lawrence in Vietnam. Austin confirms that it was Spota's car that hit and killed Lawrence during their footchase; Spota's car is actually yellow but had recently been painted blue. Caldwell learns that the water company Spota works for is owned by Arthur Peale, thus confirming that Spota, Peale, and Lawrence were working together. Austin and Caldwell follow Spota during his daily water deliveries. Spota makes a delivery to Travis Air Force Base. Under surveillance by Austin and Caldwell, Spota picks up a bottle of water that was transported to the Air Force base from the Philippines.Austin and Caldwell follow Spota and the bottle of water back to the water company. Unsure what is in the water bottle that makes it so valuable, Austin and Caldwell see the edges of the conspiracy come together. Spota, Lawrence and Peale all knew each other in Vietnam. It appears that Spota picked up a delivery of water from the Philippines, but accidentally left that water bottle in the storeroom at the Presidio. When he realized his mistake, he went back to retrieve it. Lynch surprised him during the break-in and she was shot.Just as they figure the scope of the robbery and murder, they see Maclure drive up to the water company. With a terrible realization, Caldwell figures out that Peale and Lawrence would have needed someone like Maclure to carry out the smuggling, because Maclure had excellent contacts within the US military in Asia. Inside the water company, Spota and Peale open the water bottle that came from the Philippines, revealing that diamonds were smuggled inside--the diamonds being nearly invisible in the clear water. Maclure comes in and surprises them holding his own .45 pistol from the base museum. Peale reveals that Lawrence was blackmailing Maclure about something Maclure did while in Vietnam. Peale tries to convince Maclure to let the smuggling operation continue. But Maclure is disgusted with himself and heartbroken over the death of Lynch, whom he knew. He says the smuggling must stop, but then is stripped of his gun by Peale's men. Just as Peale is about to kill Maclure, Caldwell and Austin enter the water company to save him. A gun fight ensues, during which Peale and his men are killed, and Maclure is fatally wounded while trying to pass his pistol to Caldwell.Caldwell asks Austin to delay his police report by 48 hours to give Caldwell time to bury Maclure with his honor intact. Austin agrees and the final scene is at a military cemetery where Caldwell tearfully eulogizes Maclure. At the end of the film, Caldwell reconciles with Donna and grudgingly admits Austin into the family.