Multiple realities
(covers information from several alternate timelines)

Intruder alert was an alert status on Federation starships and space stations. It could be declared at any time, by computer or any crewmember upon detecting an intruder on board. It could also be activated automatically based on predefined criteria, such as entering a restricted area. The alert was announced by audio and crewmembers were expected to take appropriate action. In 2266, a security alert 3 announced a possible intruder aboard a vessel. (TOS: "Dagger of the Mind") Intruder alert was also known as "general quarters security condition three". (TOS: "The Man Trap")

In 2269, Spock announced an intruder alert in response to the crew of the USS Enterprise's realization that Carter Winston was actually a Vendorian spying for the Romulans. (TAS: "The Survivor")

In the mid-2270s, the Enterprise computer detected an intruder on deck five (the Officers' Quarters) and announced an intruder alert. Captain James T. Kirk commanded a security team to the deck, where he determined that the intruder was a probe, in the form of Ilia, sent by V'ger. (Star Trek: The Motion Picture)

In 2364, Wesley Crusher rushed to the bridge to warn of an impending intruder alert he detected while experimenting with ship's long range sensors. The warning was immediately confirmed by Tasha Yar and an audible alert over the ship's Comm. This type of alert was later referred to as a Proximity alert or Proximity alarm to differentiate an approaching vessel from a shipboard intruder. (TNG: "The Battle")

In 2367, Captain Jean-Luc Picard attempted to sound an intruder alert when "Ardra" appeared in his quarters. (TNG: "Devil's Due")

In 2369, Commander William T. Riker initiated intruder alert when armed Ferengi boarded the USS Enterprise-D. (TNG: "Rascals")

That same year, Miles O'Brien activated the intruder alert and called a security team into his quarters when the fictional character Rumpelstiltskin appeared in Molly's bedroom. (DS9: "If Wishes Were Horses")

In 2370, Doctor Julian Bashir called intruder alert when he suffered an attack from a tentacle while in the infirmary, which, unknown to anyone at the time, was actually an out-of-control Odo. (DS9: "The Alternate")

In 2371, when the energy patterns of the Komar and Chakotay were forcing the crew of the USS Voyager to perform actions against their will, Tuvok initiated an intruder alert. (VOY: "Cathexis")

In 2372 of an alternate timeline, the computer of the USS Yellowstone declared an intruder alert and that there was an unauthorized launch in progress when Ensign Harry Kim and Tom Paris hijacked it. (VOY: "Non Sequitur")

That same year, Chakotay declared an intruder alert as Kazon boarding parties breached Voyager through its shuttlebays following a coordinated attack. (VOY: "Basics, Part I")

Rom activated an intruder alert which was detected by Damar after Odo failed to deactivate the alarms on a conduit leading to an EPS feed. (DS9: "Favor the Bold")

In 2373, Captain Kathryn Janeway underwent a mind meld with Lieutenant Tuvok to try to determine the source of an apparent repressed memory. In the meld, she was sent to the bridge of the USS Excelsior in 2293 in Tuvok's memory. A disruption of the meld caused the Captain Hikaru Sulu of the memory to notice her presence and he declared an intruder alert, but she and Tuvok solved the problem by returning to an earlier stage of the memory, in which she was able to steal an appropriate Starfleet uniform to blend in. (VOY: "Flashback")

That same year, Janeway called security for an intruder alert when she discovered Q within her quarters. She received no response and Q commented that there was "no need to call for room service" as he had already ordered, indicating champagne. Janeway repeated her order for an intruder alert but again got no response and Q commented that he had "taken the proverbial phone off the hook." (VOY: "The Q and the Grey")

Also that same year, when the holographic character Marayna appeared in Tuvok's quarters despite having apparently been deleted, Tuvok called for an intruder alert, but she used her control of the Voyager computer system to silence it. (VOY: "Alter Ego")

Additionally, when The Doctor realized that macroviruses had infested Voyager's mess hall, he declared an intruder alert on deck 2, Section 13. (VOY: "Macrocosm")

In Lieutenant Tuvok's Insurrection Alpha holoprogram, the Voyager computer declared an intruder alert on deck 8 when the Lieutenant Tom Paris and Captain Kathryn Janeway of the program transported there. (VOY: "Worst Case Scenario")

In an alternate timeline, Neelix helped repair the internal sensors aboard the USS Voyager after they had been seriously damaged due to repeated Krenim attack. He wanted to try several variations on the audio warning for Intruder Alert sound, but security chief Tuvok ordered him to keep the standard Intruder alert sound. (VOY: "Year of Hell")

Tuvok initiated an intruder alert and called for security to deck one when the two astronauts from the planet that Voyager was trapped above in orbit transitioned into Voyager's timeframe. (VOY: "Blink of an Eye")

In 2374, the crew of Voyager initiated an intruder alert when they discovered that a member of Species 8472 had penetrated their hull and invaded the ship. (VOY: "Prey")

That same year, Chakotay called an intruder alert when a Ramuran tracer was discovered in his quarters. (VOY: "Unforgettable")

In 2375, when the Borg Queen appeared to Seven of Nine while she was regenerating, Seven attempted to contact security for an intruder alert. There was no response and the Borg Queen explained that she was speaking directly to her through her neural transceiver and their thoughts were one. (VOY: "Dark Frontier")

In 2376, Lieutenant B'Elanna Torres jokingly declared "intruder alert" when her old boyfriend Lieutenant Maxwell Burke accessed a command station in engineering without her prior authorization. (VOY: "Equinox")

Later that year, in an alternate timeline, Captain Janeway declared an intruder alert on Voyager as a troubled Kes approached engineering. (VOY: "Fury")

In 2377, Lieutenant B'Elanna Torres declared an intruder alert when she and Seven of Nine found Fantome hiding in one of Voyager''s cargo bays. (VOY: "The Void")

In 2378, the Delta Flyer computer reported an intruder alert when the Talaxian child Brax snuck aboard the vessel. (VOY: "Homestead")

In 2379, an intruder alert was declared by Lieutenant Commander Worf when the Remans boarded the USS Enterprise-E on deck 29. (Star Trek Nemesis)

In 3074, a version of The Doctor activated from the EMH backup module by a Kyrian tried to call Voyager's bridge and declare an intruder alert, not realizing that he was in the Museum of Kyrian Heritage and those he was trying to alert were likely long dead. (VOY: "Living Witness")

According to the shooting script for Star Trek: The Motion Picture, an intruder alert was declared by the computer when the probe first entered the Enterprise; however, the lines were trimmed from the theatrical cut of the film.
Community content is available under CC-BY-NC unless otherwise noted.