(covers information from several alternate timelines)
Mutiny can be defined as an unlawful attempt by military personnel to seize or overthrow military authority. For purposes of this article, mutiny refers specifically to any attempt by a starship's crewmembers to illegally take control of the vessel from its captain.
Historically, mutiny was, and still is considered to be one of the gravest offenses that a member of the military can commit. In the past, those accused of it would face a court martial, and if convicted, faced severe punishment, up to and including capital punishment (though by the 22nd, 23rd, and 24th centuries, capital punishment had been abolished and thus was not a sentencing option for convicted mutineers). Acts of mutiny in present day Starfleet were considered nearly unimaginable and extremely rare. (TOS: "The Tholian Web")
Garth of Izar
Fleet Captain Garth of Izar told Captain Kirk that following his learning of the techniques of cellular metamorphosis on Antos IV, the crew of the starship he commanded mutinied against him. Garth, who had gone insane, ordered the destruction of Antos IV, but the crew did not carry out his orders and relieved him of command. Garth was committed to a Federation rehabilitation colony on Elba II. (TOS: "Whom Gods Destroy")
The Pegasus incident
In 2358, the USS Pegasus, under the command of Erik Pressman, had been testing a phasing cloaking device. This highly secretive project was against the Treaty of Algeron and was extremely dangerous to the ship's crew.
This dangerous situation came to a head with most of the Pegasus officers holding a mutiny against Pressman. William T. Riker was the only bridge officer to defend the captain; however, a few other crew members joined Riker and Pressman from various sections of the ship. The Pegasus seemed to explode moments after their escape pods were launched. The mutineers went down with the ship.
The Starfleet Judge Advocate General later investigated the Pegasus incident, but the survivors withheld all information about the phasing cloaking device. The Starfleet Judge Advocate General was only able to conclude that there had been a mutiny aboard the Pegasus prior to its destruction and that it was likely the survivors were not telling the complete truth. It was recommended that there be a further investigation; however, due to the sensitive nature of the phasing cloaking device experimentation, Starfleet Intelligence quickly classified the report and no follow-up was ever conducted. (TNG: "The Pegasus")
The Telepathic Archive
The newly-discovered Bajoran wormhole, which provided instant access to and from the Gamma Quadrant, inspired many exploration missions, but one Klingon expedition ended in tragic mutiny. Upon returning from the Gamma Quadrant, the cruiser was badly damaged and only its first officer survived. He was beamed aboard Deep Space 9 shortly before his ship exploded, and although he died within moments, he managed to utter one word: "Victory."
Unknown to both the Klingons and the crew of Deep Space 9, the cruiser had discovered a telepathic log from a long-dead civilization, and when the first officer was beamed aboard the station, he brought it with him. The same mutiny which had destroyed his ship became to manifest itself aboard the station as tensions between Major Kira Nerys and Commander Benjamin Sisko escalated to unusually high levels. Loyalties were split primarily along Federation and Bajoran lines, with Chief O'Brien being Sisko's closest ally but Lieutenant Dax siding with Kira. The only members of the senior staff not involved were Constable Odo and Doctor Bashir; while Odo was unaffected by the telepathic field, Bashir appeared to have been affected by someone who had been neutral or otherwise more interested in his own well being in the ancient civilization.
As Odo realized what was going on and both Kira and O'Brien courted him for his loyalty, he began to discover the cause of the mutiny as he pieced together damaged log entries from the Klingon ship. He and Bashir came up with a plan to remove the telepathic field, although Bashir was more interested in gaining a personal advantage than saving the other crew members. Odo used his favorable position among both sides to lure them both into a cargo bay, where he activated the program to remove the field. Everyone but Odo, including Bashir, appeared to suffer a massive headache when it was activated, and a purple energy field was released from their bodies. None of them remembered what had happened. Telling them to grab hold of something secure, Odo opened the cargo bay door enough to allow the field to be sucked into the vacuum of space, saving the station and its crew. (DS9: "Dramatis Personae")
The Maquis and the USS Voyager
When B'Elanna Torres attacked Joseph Carey in 2371, a number of Maquis crewmembers, including Seska and Jarvin, were in support of a mutiny if Chakotay was to perform one. This did not go forth. (VOY: "Parallax")
Vedek Teero Anaydis
In 2377, Teero Anaydis, a radical Bajoran Vedek who was determined to fight the Cardassians, engineered a plan to cause a Maquis mutiny on the USS Voyager. Teero Anaydis had been kicked out of the Maquis earlier for experimenting with mind control as a means of getting new agents. Afterward, the Dominion crushed the Maquis resistance in the Alpha Quadrant so Teero Anaydis turned his attention to the Delta Quadrant and the stranded Starfleet vessel whose crew, many of whom were Maquis, had contact with the Federation.
In 2370, he had implanted suppressed memory commands into Tuvok at a colony near the Badlands. These commands would activate when Tuvok heard a certain Bajoran chant. Teero Anaydis triggered the suppressed commands in Tuvok in 2377 by embedding a subliminal message consisting of the chant into a letter to Tuvok from his son Sek. Tuvok then used Vulcan mind melds to implant these commands into the other Maquis members of the crew. Voyager was almost taken by Teero Anaydis and his new 'recruits', however Tuvok managed to reclaim control of his mind and used the mind meld technique to stop the mutiny by returning the minds of the other Maquis crew members to normal. (VOY: "Repression")
- See also: Insurrection Alpha
In 2376, Maxwell Burke, first officer of the USS Equinox, mutinied against Captain Rudolph Ransom after Ransom had ordered the remnants of his crew to surrender to the USS Voyager. Burke wished to continue killing nucleogenic lifeforms to fuel the Equinox's enhanced warp drive, an action which Ransom initially supported, but later realized was against both Starfleet principles and his conscience. While Burke asked Ensign Marla Gilmore to take Ransom to the brig, she instead escorted him to engineering and informed him she was still on his side. Ransom arranged to beam Gilmore along with other crew members not in shielded areas to Voyager. Burke and others with him on the bridge were killed by the nucleogenic lifeforms while attempting to reach the Equinox's shuttlebay. Ransom went down with his ship. (VOY: "Equinox, Part II")
The Mirror Universe
Mutiny was a common sight in the mirror universe throughout the 22nd and 23rd centuries. Mutiny usually involved members of the crew assassinating a superior officer as a means of advancing in rank. Such officers who carried out these assassinations tended to rely on bodyguards and surprise.
In 2155, Commander Jonathan Archer, first officer of the Imperial Flagship ISS Enterprise staged the first recorded mutiny aboard in Starfleet history, by wresting control from Captain Maximilian Forrest. By rallying the support of Major Malcolm Reed and Sergeant Travis Mayweather, Archer was able to detain Forrest and bring Enterprise into Tholian space to pilfer the USS Defiant, a Federation Starship brought across an interphasic rift from 2268.
Shortly after these events, the now First Officer T'Pol waged a second mutiny, using Vulcan crewmen to extradite rightful Captain Forrest from the brig. The command crew was able to detain Archer, who was entitled to a record ten hours in the agony booth, developed by Major Reed and Doctor Phlox.
After Archer was able to successfully attain command of the Defiant and escape from Tholian space, his mutinous actions were far from over. Leaving Captain Forrest to die with Enterprise, he then brought Defiant to the front lines of the Rebellion the Empire was losing badly. With the advanced Starfleet weaponry, the 22nd century vessels were easy targets for the Defiant's phaser and photon torpedo banks.
After successfully destroying a Rebel attack force, Archers' plans doubled yet again. It was now that the former Enterprise first officer began sowing the seeds of his own ascent to the role of emperor by challenging Fleet Admiral Gardner. His downfall, however, was his Vulcan first officer, who saw that it would make things even worse for her people. She used the completely non-Human crew of the ISS Avenger to sabotage the Defiants power grid and attack. However, the quick actions of Chief Engineer Tucker allowed Defiant to raise her shields and destroy the Avenger.
When celebrating his victory with Hoshi Sato, whom he trusted implicitly, Archer found his champagne poisoned. Sato then rewarded his personal guard, Mayweather for his treachery and the former comm officer took over the late Commander Archer's plans to overthrow the Empire with the Defiant at her disposal. This cutthroat, cloak and dagger means of assassination paved the way for the Imperial crews in future years. (ENT: "In a Mirror, Darkly", "In a Mirror, Darkly, Part II")
In 2267 Pavel Chekov was a cunning schemer with designs on overthrowing Kirk as captain, to which end he enlisted several other crew members in his mutiny. By the time Chekov carried it out, the mirror Kirk had been replaced with a parallel universe duplicate who was able to defeat him. Chekov was punished with a trip to the agony booth. (TOS: "Mirror, Mirror")
In the alternate reality, James T. Kirk attempted a mutiny against Spock when he disagreed with Spock's decision to take the USS Enterprise to the Laurentian system rather than go after the Narada and Nero. His mutiny failed and Spock marooned him on Delta Vega, but he returned to the Enterprise with the help of Spock Prime and Montgomery Scott. Once there, he successfully took command of the ship by forcing Spock to prove that he was emotionally compromised, following directions from Spock Prime. As Kirk had been made acting first officer, when Spock resigned he automaticaly became acting captain. After Spock regained control of his emotions, he returned but defered to Kirk's command and seemed to function as his first officer. Kirk seemed to suffer no reprisals from his mutiny and is later given offical command of the ship. (Star Trek)