- Being Watched: 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 shes being watched, the lights go out and when she desperately reaches for the hatch to an upper level its 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.
- Booby Trap: Admiral Chegwidden's girlfriend, Judge Delaney, is killed by a booby trap, set up by an old rival from The Vietnam War, in front of him on his own porch in the season 2 episode "Ghosts".
- Cruel and Unusual Death:
- In "Crossing the Line" (second season), Lieutenant Isaacs loses control of her jet while attempting to land, and she and 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 Russian crew aboard the diesel submarine Al-Qaeda bought from Iran succumbs to radiation poisoning because the dirty nuke is unshielded. Complete with Incurable Cough of Death.
- 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 Adult Fear 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).
- Coming in Hot: Unlike Top Gun which skirted this particular aspect of carrier aviation altogether, this show makes no bones about how dangerous carrier landings are, particularly night traps. Harm's backstory involves a botched night trap that killed his Guy in Back, a Lt Isaacs who was grounded for unsafe flying scorches to death after ejecting from her failed landing, another aviator "dead sticks" his plane in because a different crewman' mistake left him with inadequate fuel, Harm again has to land an aircraft that is leaking fuel and has one engine flamed out.
- Backdoor Pilot "Ice Queen" gives us the very epitome of a Bus Crash, pictured above, Lieutenant Loren Singer's remains are found after a Boy Scout accidentally shot an arrow into them. The poor woman's been dead for two or three weeks judging from decomposition, and crows have completely eaten away her face, leaving a bare skull with heaps of rotten flesh mangled around it. She was a rotten person to the core, so the creators used her as cannon fodder to set up a new series, knowing nobody would miss her. It's also a stark moment where the show kills off a character in such a grisly manner to show that they mean it and there is no going back... and to top it all off, she's also used as the first murder victim for NCIS, where remains like this are found on a regular basis, often in even worse condition than hers.Gibbs: (sounding mildly disturbed) What happened to her face...? It's too cold for larva...
- Unfriendly Fire: Multiple episodes deal with this all too real horror faced by military personnel. People are shot, strafed, bombed, hamburgered by artillery not by the bad guys but by people who were supposed to be on their side.
Nightmare Fuel / JAG