* BeingWatched: In "Skeleton Crew", Commander Alison Krennick, while investigating the murder of a female officer, is lost in the corridors aboard the aircraft carrier USS Seahawk. She suddenly feels that she’s being watched, the lights go out and when she desperately reaches for the hatch to an upper level it’s stuck. Then it suddenly opens and a Marine guard is on the other side and he goes down to see if there is anyone there, but he finds nothing. It is implied by the camera angles that someone actually was following her, but we never get to see who it was.
* BoobyTrap: Admiral Chegwidden's girlfriend, Judge Delaney, is killed by a booby trap, set up by an old rival from TheVietnamWar, in front of him on his own porch in the season 2 episode "Ghosts".
** In "Crossing the Line" (second season), Lieutenant Isaacs loses control of her jet while attempting to land, and she and [[GuyInBack Skates]] eject just before the plane slams into the carrier's fantail. Skates just barely misses landing on the deck and ends up snagged on the railing of the carrier (Harm barely rescues her from going overboard). Isaacs... is less lucky, as she ends up parachuting directly into the burning wreckage of her own plane.
** In "Death Watch" (third season), Commander Holbarth, the murderer of Harm's academy classmate in "Skeleton Crew", fell into the water and was crushed to death between the hull of a destroyer and the dock.
** In "Enemy Below" (seventh season), the [[RenegadeRussian Russian crew]] aboard the diesel submarine Al-Qaeda bought from Iran [[ConvenientTerminalIllness succumbs to radiation poisoning]] because the dirty nuke is unshielded. Complete with IncurableCoughOfDeath.
*** From the same episode, the [[ForeShadowing ongoing plotline]] of [[ParanoiaFuel landmines in Afghanistan]] is capped off with [[spoiler: Lt. Bud Roberts]] stepping on a landmine at the very end of the episode.
** In the pilot episode, Lt. Arutti is thrown overboard and drowns. Upon performing an autopsy, the coroner finds that she survived the fall, suffered internal injuries, but was conscious and ingested water while trying to swim despite her injuries. According to the coroner, her death was slow and excruciatingly painful. Even worse is that she did nothing to warrant her murder. A crewman with a grudge mistook her for someone else in the dark and she was effectively killed entirely at random.
* "Pilot Error" highlights the AdultFear that spouses and family members of military personnel face: That their loved ones will be gone for months at a time and could die without warning, in addition to more mundane concerns about infidelity (the deceased pilot and his female wingman were very close, and rumors abound that they may have had an affair).