The Maquis were a paramilitary group that were formed in 2370 as a result of resistance to the new treaty between the United Federation of Planets and Cardassian Union, which ordered the resettlement of millions all over the newly formed Demilitarized Zone.
The Maquis came from populations who lived on planets under Cardassian control that were constantly abused and were subjected to hate crimes and attacks on their families, businesses and property without protection from the Federation. (TNG episode: "Journey's End")
Matters further escalated when it was discovered that Cardassian Legate Parn was responsible for shipping weapons into the DMZ on small freighters. The Maquis finally mobilized and smuggled in weapons of their own into the DMZ. After their demolitions expert William Patrick Samuels was captured on Deep Space 9 and executed by agents loyal to Cardassian Gul Aman Evek, the Federation got involved and a skirmish war began. The first interplanetary attack by Maquis forces was made by former Starfleet officer, Cal Hudson, who led two raiders to attack a hidden Cardassian weapons cache on Bryma. The attack was turned back, but it exposed the truth about the Cardassians colonists' secret military build-up.
The Maquis themselves consisted primarily of former citizens of the Federation whose homeworlds were ceded to the Cardassians by the treaty. Their roster soon expanded to included ex-Starfleet officers and soldiers (such as Cal Hudson, Chakotay, B'Elanna Torres, Tom Paris and Thomas Riker) who had become disillusioned with living in the "paradise" of Federation space while thousands suffered and died in the DMZ. They often supplied weapons (such as Quark), information (such as Razka Karn) and supplies (such as Kasidy Yates) to the Maquis. At its height, the movement was comprised of some 250,000 active members and un-told thousands of sympathizers and an assortmant of 390 ships, each in a varied class or type. (DS9 episodes: "The Maquis, Part I", "Indiscretion", "For the Cause"; VOY episode: "Caretaker")
The Maquis also had an extensive network of spies throughout the Federation, DMZ and Cardassian space (of which Kasidy Yates was one). Starfleet Intelligence tried infiltrating the network and gaining names, but was mostly unsuccessful. (DS9 episode: "For the Cause")
The Maquis were also infiltrated by spies from different powers (such as Seska from the Cardassians and Tuvok from the Federation) although on occasion spies deserted their ranks and joined permanently (an infamous case involving Ro Laren). (TNG episode: "Preemptive Strike"; VOY episodes: "Caretaker", "State of Flux")
The "war" continued, as the Maquis's strength grew and Cardassian casualties grew higher, the Cardassian Central Command grew increasingly violent and demanded to be allowed into the DMZ with a fleet to "disarm" (exterminate) every colony in the DMZ, but the Federation protected the Maquis from the Cardassians behind the shield of diplomacy and allowed them a free reign. (DS9 episode: "Defiant")
The Maquis knew about reprisals against their friends and families, who (for the most part) lived in the DMZ. To this end, a Bajoran cell leader named Arak Katal rallied separate Maquis factions and established a base on Tevlik's Moon. This provided the Maquis with not only a stable powerbase, but a safe haven to hide their families from reprisals and allow them to continue the war without personal feelings imposing on their separate missions (the base was named Tevlik's Moonbase). Other important bases were the Terikof Belt outposts that served as an attack staging ground against Cardassian space, and an emergency outpost that was built on the remote Badlands planet of Athos IV. The Maquis established at least 61 bases in the Badlands, a section of the DMZ covered in plasma storms, and provided ideal hiding places. (VOY novels: Homecoming, The Badlands, Part III)
One of the most infamous attacks on Cardassian space was made by cell leader Thomas Riker in 2371, when he stole the USS Defiant and launched a hit-and-run attack on the Union. Though it nearly brought the Cardassian fleet to the DMZ and the mission's objective failed, it set the scene for the destruction of the Obsidian Order and convinced more Starfleet personnel of their good intentions, yet not their superiors who still regarded the Maquis as a "band of traitors and criminals". (DS9 episode: "Defiant")
However, several members of the Maquis grew frustrated at the limits the Maquis leaders were willing to go to achieve victory, and sought out more powerful ways to inflict damage on the Cardassian Union. Such cases included the Andorian Maquis member Tharia ch'Ren using a Malkus artifact to inflict catastrophic environmental damage on planets of the Cardassian Union, another was when Ro Laren/Codename "Architect" was dispatched to stop a Maquis extremist named Aela from assassinating Gul Engor and destroying Deep Space 9. Ro also delivered crucial food and medical supplies during the affliction of the "Wrath of the Prophets" disease that threatened the populations of Bajor and Deep Space 9. The longest reaching event was when a fanatical Maquis, Vedek Teero Anaydis, was expelled from the organization for experimenting in mind-control to recruit agents, he vowed revenge on his former comrades. He tracked down Starfleet spy Lieutenant Tuvok on a planet in the Badlands and placed a mind-control message in his subconscious that would be activated several years later. These incidents were put down by their fellow Maquis and sympathetic Starfleet officers, helping cement the ideal of peaceful coexistence between the Maquis and Federation. (VOY - The Brave and the Bold, Book Two novella: The Third Artifact; TNG novel: Rogue Saucer; DS9 novel: Wrath of the Prophets; VOY episode: "Repression")
During the Klingon-Cardassian War, the Cardassian's devastated industry sought aid from the Federation, who arranged to provide them with 12 industrial replicators. The Maquis learned of this and, seeking to keep the Cardassians crippled, arranged to have their agent aboard Deep Space 9, Lieutenant Commander Michael Eddington, capture the replicators and deliver them to a Vulcan freighter under their control. Captain Benjamin Sisko eventually learned of this and rushed to stop him, but Eddington escaped on the freighter with the replicators into the DMZ. Not only did this keep the Cardassians weak and provide immense engineering support to the Maquis, but it also propelled Eddington into the supreme leadership position of the entire Maquis movement. (DS9 episode: "For the Cause")
Eddington re-surfaced at the command of eight raiders and, after stealing chemicals and equipment for biogenic weapons from Bolian and Breen freighters along the border of the DMZ, planned to sterilize every DMZ colony occupied by the Cardassians, which would put the entire zone under their control. Eddington began his attack and sterilized three Cardassian colonies before being forced to surrender himself and the remainder of the weapons to Captain Benjamin Sisko when he was faced by a similar Federation attack on the Maquis colonies. (DS9 episode: "For the Uniform")
Despite the capture of their leader Eddington, the rest of the movement went on, this time having individual "cell" leaders that commanded them. One such case was Chakotay, who commanded his crew aboard the Val Jean on several missions on Cardassian space, one such attack, in which a Cardassian station was destroyed, forced the Val Jean into the Badlands under pursuit from Gul Evek and led him and his cell to be propelled into the Delta Quadrant. (VOY episode: "Caretaker")
With the Cardassians weakened even further by internal problems, the Maquis realized they were winning, and with a free hand in the DMZ, planned to declare their independence from both superpowers.
All this was undone, however, when rogue Gul Skrain Dukat arranged for the remnants of the Cardassian Union to join the Dominion, the Gamma Quadrant superpower that was able to provide overwhelming military and economic support to the Union. Dukat, now Cardassia's new leader, promised that the new Dominion-Cardassian alliance would not only drive the Klingons out of Cardassian space, but also wipe out every Maquis in the DMZ within five days. Dukat would keep his promise. (DS9 episode: "By Inferno's Light")
On stardate 50953.4 in 2373, the combined Dominion-Cardassian fleet launched and overran the DMZ within the space of three days (later known as the Three-Day-Massacre). With only small fighters, freighters, courier ships and raiders to fight with, the Maquis were no match and their guerrilla tactics failed against overwhelming waves of cloned Jem'Hadar soldiers. The Dominion took no prisoners.(VOY episode: "Hunters")
Every single Maquis base was exposed, especially Tevlik's Moonbase, and destroyed when Arak Katal, now revealed to be a Changeling infiltrator, supplied the Female Changeling with the locations of the Maquis hiding places.
The surviving Maquis members halted their combined retreat to make their final stand at their emergency outpost on Athos IV. Unfortunately, the Jem'Hadar landed on the planet and killed the majority of the surviving members within one day of the attack being launched. After two days of imprisonment, the surviving Maquis were freed from captivity in their own base by Captain Benjamin Sisko and newly-released Michael Eddington and fled the planet to safety, although Eddington himself died getting the others out. (DS9 episode: "Blaze of Glory")
Only several hundred Maquis remained, whether in scattered groups, Chakotay's cell, or in prison. All of them were pardoned and joined Starfleet's efforts to fight the Dominion later that year.(VOY episode: "Hunters")
Known cells who survived were Chakotay's (60 members), Eddington's (13 members), Hudson's (5 members), Kaz's (17 members), Riker's (6 members), Ro's and Sveta's. ((VOY episode: "Hunters")VOY novels: Homecoming, Spirit Walk, Old Wounds)