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Being confined to quarters (sometimes phrased as "restricted to quarters") was a punishment that could be applied on Federation Starfleet starships and starbases. This form of discipline was generally used for more minor offenses, rather than those of a more serious nature that would require action such as being placed in the brig or a reduction in rank. On occasion, this punishment may be used as a long-term measure in special circumstances. The punishment, usually, though not always, also involved being temporarily relived of duty.
On occasion, temporary confinement to quarters was also used as a security measure to protect non-essential starship crew from an imminent threat.
In 2152, Captain Jonathan Archer restricted both Commander Charles Tucker III and Lieutenant Malcolm Reed to quarters following an unauthorized exploration of the interior of the automated repair station, stating that he was beginning to agree with Reed's recent assessment that security on the Enterprise NX-01 had become lax. It was uncertain how long this punishment lasted, however, as both were called to duty following the discovery of the apparently dead Ensign Travis Mayweather. (ENT: "Dead Stop")
In 2154, when Captain Jonathan Archer was suffering from reverse-imprinting on Xindi-Insectoid eggs, he confined both Subcommander T'Pol and Lieutenant Malcolm Reed to quarters and threatened the same punishment for Charles Tucker III after each spoke against his actions in protecting the eggs. (ENT: "Hatchery")
That same year, Commander Charles Tucker III ordered Commander Kelby confined to quarters after he displayed mildly insubordinate behavior toward him. When Kelby resisted, Tucker told him that it was either that or the brig. (ENT: "Bound")
In 2268, Captain James T. Kirk confined Ensign Garrovick to quarters and relieved him of duties after he hesitated in firing upon a dikironium cloud creature. Doctor Leonard McCoy felt the punishment was too harsh, but Kirk noted that one man had been killed and another might die. Garrovick, however, left his quarters after a general call to battle stations and Kirk, realizing that Garrovick had simply made a mistake, and one that ultimately was not the cause of any deaths, chose to release him from his punishment and give him a chance to redeem himself. (TOS: "Obsession")
That same year, Captain James T. Kirk confined several members of the crew of the USS Enterprise to quarters following a barroom brawl on Deep Space Station K-7, including Chief engineering officer Montgomery Scott. Although this was supposed to be a punishment, Scott was secretly delighted as he had resisted taking shore leave and being confined to quarters gave him a chance to catch up on his reading of technical journals. (TOS: "The Trouble with Tribbles"; DS9: "Trials and Tribble-ations")
In 2366, Doctor Paul Stubbs was told to return to his quarters immediately by Ensign Wesley Crusher during a red alert on the USS Enterprise-D, suggesting that this may have been standard for non-essential personnel during emergency situations on the vessel. Guinan later commented to Crusher that she had never been good at being confined to quarters, something that any of her husbands could attest to. (TNG: "Evolution")
In 2370, Lieutenant commander Data threatened to have Lieutenant commander Geordi La Forge confined to quarters for the duration of the mission to investigate the wreckage of the USS Raman if Geordi persisted in using an interface probe to search for his mother against the orders of Captain Jean-Luc Picard. Realizing how important the issue was to Geordi, though, he chose to try to help keep him safe instead, stating that he couldn't have him confined to quarters for something he had not yet done. (TNG: "Interface")
That same year, Commander Benjamin Sisko ordered all non-essential personnel on Deep Space 9 restricted to quarters and called for red alert after a series of attacks on the station that unknown to anyone at the time, including himself, were done by Constable Odo, under the influence of toxic gas. (DS9: "The Alternate")
In 2371, following an incident in which Lieutenant B'Elanna Torres broke Lieutenant Joseph Carey's nose, Ensign Seska reported a rumor that all Maquis crewmembers on the USS Voyager were going to be restricted to quarters when not on duty, but Commander Chakotay told her this wasn't true. (VOY: "Parallax")
In 2372, Captain Benjamin Sisko confined Lieutenant commander Worf to his quarters during those times he was not on duty on the USS Defiant following a brawl involving a number of Jem'Hadar. First Omet'iklan was not impressed with Sisko's choice of discipline, believing that he should have killed Worf, but Sisko felt that a dead man could not learn from his mistakes. (DS9: "To the Death")
That same year, Crewman Lon Suder was discovered to have murdered crewmate Frank Darwin on-board Voyager. Though Suder's crime was of the most extreme nature, Voyager's unusual circumstances of being stranded in the Delta Quadrant caused Captain Kathryn Janeway to choose to keep Suder confined in his quarters under maximum security containment for the duration of their journey home. (VOY: "Meld") This punishment continued up until Suder's death later that year. (VOY: "Basics, Part II")
In 2373, Captain Benjamin Sisko confined Cadet Nog and his son to quarters after they accused Kai Winn Adami of burglary and kidnapping and Jake claimed that they had gotten a little drunk. In fact, the two were investigating the disappearance of Doctor Elias Giger, who was in possession of a Willie Mays baseball card that Jake wished to give to his father. (DS9: "In the Cards")
In 2374, a number of both the Cardassian and Jem'Hadar aboard the temporarily Dominion-occupied Deep Space 9/Terok Nor were confined to quarters pending disciplinary hearings following an incident involving a missing PADD that was actually caused by the Deep Space 9 Resistance. (DS9: "Behind the Lines")
That same year, Gul Damar suggested to Gul Dukat that his daughter Tora Ziyal be temporarily confined to quarters, as he believed her to be part of the Deep Space 9 Resistance, but Dukat resisted the suggestion. (DS9: "Sacrifice of Angels")
Also that same year, a holographic simulation of Captain Benjamin Sisko supposedly relieved the senior staff of Deep Space 9 of duty and confined them to quarters pending an investigation by Internal Affairs. This, however, was all a ruse created in a holosuite by Luther Sloan to test Doctor Julian Bashir and Bashir was, in fact, the only one who suffered any sort of confinement. (DS9: "Inquisition")
In 2376, Captain Kathryn Janeway confined Captain Rudolph Ransom and the other surviving members of the USS Equinox to quarters on Voyager after learning of their killing of nucleogenic lifeforms as a source of warp power for the Equinox. Ransom pleaded for leniency, stating that they were only following his orders, but Janeway replied that this was their mistake. Almost all of them later escaped to the Equinox and attempted to flee Voyager. Later, after Janeway took extreme measures to get information regarding Ransom out of Crewman Noah Lessing, Commander Chakotay objected vociferously to her actions and she relieved him of duty and confined him to his quarters. Ultimately, the remaining Equinox crew that survived the incident were stripped of rank and made to serve on Voyager as crewmen. (VOY: "Equinox", "Equinox, Part II")
That same year, Janeway confined Ensigns Harry Kim and Tom Paris to quarters after they became drunk and participated in what they believed to be a Kinbori version of tennis and became involved in a brawl. She seemed mildly amused however, asking if they won they fight. (VOY: "Survival Instinct")