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Safety protocols were present to prevent serious injury of the people inside a simulation. This meant that weapons fired within the simulation would not be able to kill or that the computer could prevent dangerous situations when testing a new ship design.
Safety protocols could be overruled if the person in question had the correct access codes. It was also possible for a holoprogram to disable the safety protocols if it was programmed to do so. (VOY: "Worst Case Scenario") A malfunction in the ship's main computer could render the safety protocols inoperative. (TNG: "A Fistful of Datas")
In 2364, when a Jaradan probe inadvertently caused a malfunction in the safety protocols Whalen was shot and seriously wounded by Cyrus Redblock's henchman Felix Leech who also struck Jean-Luc Picard with his Pistol busting his lip for striking him earlier. (TNG: "The Big Goodbye")
In 2369, the holodeck safety protocols were rendered inoperative due to a malfunction in the USS Enterprise-D's main computer. This resulted in injury to Lieutenant Worf and placed him, Counselor Deanna Troi and Worf's son, Alexander Rozhenko, in continued jeopardy, as the computer also did not respond to their request to terminate the Ancient West simulation that they were engaged in. (TNG: "A Fistful of Datas")
That same year, Data attempted, but was unsuccessful, to override the holodeck safety protocols while recreating an unusual Borg attack on the Ohniaka III Research Station where Data became, seemingly spontaneously, angry. After attempting to increase the simulated Borg's strength by 30 percent, Data informed Geordi La Forge that the computer required the voice authorization of two senior officers to disable the safety routine and asked for his help in overriding the it. La Forge refused, but this was the only instance where two individuals were needed to disable the protocols. Data's rank was presumably insufficient to complete the procedure alone, even though Lieutenant commander was sufficient aboard other vessels like USS Voyager (VOY: "Extreme Risk"). It may have been a requirement unique to the USS Enterprise-D, or the requirement may have changed between this and other points in time. (TNG: "Descent")
In 2372, Julian Bashir and Elim Garak ran the holoprogram Julian Bashir, Secret Agent together. While fighting Falcon and his men, Bashir noticed that Garak was bleeding. Garak noted that the holosuite's safety protocols must have been turned off. (DS9: "Our Man Bashir")
While trying to evade the Borg on the USS Enterprise-E, Captain Jean-Luc Picard and Lily Sloane retreated into one of the ship's holodecks, where Picard ran a holoprogram of the Dixon Hill series. He was able to kill both of the Borg who were following him with a submachine gun after turning off the holodeck safety protocols. (Star Trek: First Contact)
In 2373, General Martok told Julian Bashir he had deactivated the safety protocols of a holosuite on Deep Space 9, leading to an injury, although he had in fact been injured by Worf. (DS9: "Soldiers of the Empire")
In 2373, the safety protocols were disabled as part of Ensign Seska's revised Insurrection Alpha program. Her holographic form informed Lieutenants Tuvok and Tom Paris of this at the beginning of the program stating that it meant "...if I shoot you, and I am going to shoot you, you'll die." Later, after Paris stated that nothing that was happening in the program was real, she had a holographic Chakotay phaser him in the arm and taunted "Next time, you'll believe me when I tell you the safety protocols are off." (VOY: "Worst Case Scenario")
In 2374, the holographic safety protocols were disabled by the Hirogen when they subjected the Voyager crew to a number of dangerous simulations. The Doctor urged that they be reactivated, as a number the ship's crew had been seriously injured. Karr, however, refused, as he felt it would eliminate the challenge of the hunt. (VOY: "The Killing Game") Later, when Captain Kathryn Janeway came up with a plan to disable the neural interfaces that were controlling the crew by using holographic explosives, she noted that with the safety protocols offline they were as good as the real thing. Later, as a number of Hirogen had been killed, the Hirogen medic urged Karr to enable the safety protocols, but at this point it was no longer possible, as the holodeck had been too badly damaged. (VOY: "The Killing Game, Part II")
In 2375, after learning of the Maquis' destruction in the Alpha Quadrant, B'Elanna Torres began running dangerous holodeck programs on the USS Voyager with the safety protocols turned off. (VOY: "Extreme Risk")
On Voyager's holodeck, Ensign Tom Paris noted a particular limitation when Captain Kathryn Janeway posed as Queen Arachnia, that the safety protocols couldn't prevent her from being restrained, nor from being thrown in Chaotica's Dungeon of Pain. (VOY: "Bride of Chaotica!")