At the beginning of NCIS Season 17, Episode 12 “Flight Plan”
the order to shoot down an F-18 flying off course. Shooting down a plane is the protocol to save a populated area.
Then: A Navy pilot puts her aircraft in the sea off North Carolina. Her shipmates believe she was a victim of hypoxia but NCIS finds the corpse of her ex-lover in her quarters aboard ship indicating murder-suicide. When Kasie determines that the pilot actually ejected before her aircraft crashed the team begins a “manhunt” to track her down.
Reminds me of an old OLD Steve Canyon TV show “Operation Intercept” Episode aired Mar 31, 1959” where he has to shoot down an American Plane headed for the USSR.
If this is the one I recall from decades ago, some target shooters accidentally shot holes in the aircraft causing those aboard to die in flight.