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(covers information from several alternate timelines)
Handcuffs, manacles, or shackles – known colloquially as irons or cuffs – were a type of restraint that limited an individual's wrist movement.
In 1944 of an alternate timeline, Jonathan Archer wore handcuffs while being transferred by Nazis through a wooded area in Nazi-occupied New York, in a truck. Later, handcuffs were used to imprison Charles Tucker III and Travis Mayweather, shortly after they were captured by the Nazis. (ENT: "Storm Front")
In 2151, a team of Ferengi successfully subdued the crew of Enterprise NX-01 and boarded the ship with the intent of stealing anything of value. After they were unable to locate a vault aboard the craft, they revived Captain Jonathan Archer to question him, but not before handcuffing him to a hand hold in one of Enterprise's launch bays, to prevent his escape. Thereafter, one of the Ferengi, Krem, uncuffed Archer so he could carry goods from Enterprise onto the Ferengi ship but later shackled him to another hand hold in a corridor aboard Enterprise in order to bring him some food and a drink from the vessel's mess hall. While Krem was gone, Commander Tucker covertly tried to release Archer's bonds with a small lock pick but doing so proved too difficult and Krem soon returned. He again took the shackles off Archer, so he could continue the manual labor. When Archer refused to do any more work, Krem once again handcuffed him to a hand-hold. Sub-Commander T'Pol thereafter stole the key to the shackles from Krem and eventually freed Archer, him ordering her to "open these things." Except for Krem, all the Ferengi were subsequently shackled aboard their own ship as it departed from Enterprise. (ENT: "Acquisition")
After Menos was finally captured, he was shackled, in an outpost on a moon of Pernaia Prime, by his captors: Captain Archer, Sub-Commander T'Pol, and Ensign Travis Mayweather. When Menos started a fire inside the outpost, T'Pol took off his manacles. She was about to refasten them round his wrists when he managed to escape. (ENT: "The Seventh")
In 2153, Archer admitted to Phlox that he himself hadn't been "looking forward to throwing [Phlox] in irons," after he and the physician were in dispute over the medical care of Hudak. (ENT: "The Breach")
In 2259 of the alternate reality, Khan Noonien Singh was handcuffed after surrendering to Captain Kirk and party on Qo'noS and was placed in the USS Enterprise's brig. Afterwards, he was moved to sickbay still handcuffed. (Star Trek Into Darkness)
In 2268, Captain James T. Kirk threatened to hold Federation Undersecretary for Agriculture Nilz Baris in irons if he did not "shut up" and cease his complaints about Kirk's actions at Deep Space Station K-7. (TOS: "The Trouble with Tribbles")
In 2293, Klingon General Chang ordered the arrest of Captain Kirk and Doctor Leonard McCoy for the assassination of Chancellor Gorkon. They were subsequently placed in handcuffs until their trial. However, it was later revealed that Chang had orchestrated the whole event, and they were released, cleared of all charges. (Star Trek VI: The Undiscovered Country)
In 2367, the crew of the Federation freighter Arcos was captured by the Turkana IV Alliance, following the destruction of their ship over the planet. The Alliance placed them in handcuffs incorporating a solid metal bar in between each cuff, until they were removed by a rescue team from the USS Enterprise-D. (TNG: "Legacy")
Later that year, Constable Odo handcuffed his Rakhari prisoner Croden to the rear for transport to his homeworld in the Gamma Quadrant, aboard the runabout USS Ganges. Odo later released the cuffs in order to elicit Croden's help in escaping a pursuing Miradorn raider piloted by Ah-Kel. (DS9: "Vortex")
In 2372, during the Julian Bashir, Secret Agent holoprogram, Doctor Bashir, as Patrick Merriweather, used his charm to convince Doctor Honey Bare, who was imbued with the body of Jadzia Dax due to a transporter accident, to give him her hairpin. He then used it to undo the handcuffs binding him and Elim Garak at the time. (DS9: "Our Man Bashir")
In 2373, Captain Benjamin Sisko forced Maquis leader Michael Eddington to accompany him in a Danube-class runabout to stop several missiles that were supposedly heading for Cardassian space. During their time on the runabout, the captain ensured Eddington remained in his handcuffs, though later took them off him during a firefight with Jem'Hadar forces. (DS9: "Blaze of Glory")
In 2374, following Ishka's capture by Dominion forces, Starfleet handed over the Vorta Keevan to a Ferengi rescue team comprising Quark, Rom, Nog, Brunt and Leck in order to exchange him for Ishka. During the journey from Deep Space 9 to the site of the exchange on Empok Nor, Keevan remained firmly handcuffed to the front. Similarly, Ishka was also restrained in irons prior to the exchange. (DS9: "The Magnificent Ferengi")
Later that year, Doctor Julian Bashir was handcuffed and paraded down the Promenade of Deep Space 9 to the security office, during Luther Sloan's holographic recreation of the station. The holographic representation of Captain Sisko protested, claiming a Starfleet officer shouldn't be dragged across the Promenade in irons. (DS9: "Inquisition")
In 2376, following the apprehension of Crewman Noah Lessing for his participation in a scheme to use nucleogenic lifeforms as fuel for the USS Equinox, Captain Kathryn Janeway had him placed in handcuffs and held in the USS Voyager's cargo bay, where he was subject to interrogation. (VOY: "Equinox, Part II")