Chakotay is a descendant of a tribe of Native Central American traditionalists who, unhappy with the homogenization of their ancestry by western culture, relocated to preserve their cultural identity. His ancestors left Earth to settle on Trebus - a planet near to Cardassian space, where they lived for several hundred years before Chakotay's birth.
As a young man, Chakotay followed his own path contrary to his tribes communal way of thinking. His never-ending curiosity about the Galaxy led him to get to know a lot of the Starfleet officers who patrolled the Cardassian border. He asked one - Captain Hiromi Sulu (grandson of Hikaru Sulu (TOS) to sponsor him at Starfleet Academy, and he enrolled there in 2350.
Even here Chakotay had trouble conforming to the rigid rules and protocol. Just after the end of the Cardassian Wars, around 2354, he was posted to the U.S.S. Merrimac.
Many years later while serving on the U.S.S. Gettysburg, Chakotay learned that his father had been killed during the massacre of his village by the Cardassians. Angry and bitter about a Federation that refused to act and protect it's citizens, he formally resigned his Commission to Admiral Nimembeh on 03 March 2368 and left Starfleet to join the infant rebel group who called themselves the Maquis (after Earth's World War II French Resistance movement). We later learn that he was recruited by an old friend called Sveta - who had become a Maquis after losing her own family in a Cardassian attack.
Fighting For Freedom
Though both the Cardassians and the Federation consider the Maquis unruly and dangerous outlaws, the Maquis view themselves as freedom fighters. Many are idealistic nonconformists who think their tactics are the only way to protect their families from Cardassian aggression. This suits Chakotay just fine; he wasn't quite at home on his homeworld, and he wasn't comfortable in Starfleet either. Joining the Maquis allows him to be contrary while fulfilling what he believes to be a greater good.
His leadership style with the Maquis is calm, yet firm. He isn't afraid to throw a few punches to assert his authority Maquis-style, but it takes a lot to ruffle him. He leads with gentle conviction, and trusts his crew members. In the midst of a battle against a Cardassian ship in 2371, with his Maquis Raider spacecraft, Liberty running on a 39-year-old rebuilt engine, Chakotay is assured and efficient, quietly asking his engineer Torres for more power to the engines - and he expects to get it.
His steady, fearless leadership style earns him the devotion of his Maquis crew, but it also leaves him slightly vulnerable. He inherently trusts people, judging them by their actions in the present rather than what they may have done in the past, and this makes him ripe for unknowingly harboring spies. There are two serving with him: Tuvok, a Vulcan who is spying on the Maquis for the Federation, and Seska, a Cardassian surgically altered to look like a Bajoran. When Chakotay later learns of each of their betrayals, he takes it personally - especially as at one time Seska was his lover and he feels that she used him. It's hard for Chakotay to accept that his devotion to the Maquis mission was not equalled by those he trusted with his life. But he isn't a man to wallow in his downfalls, and quickly absorbs the lesson into his psyche. When Chakotay and Tuvok find themselves serving together on the U.S.S. Voyager, Chakotay never holds the Vulcan's past actions against him. When Seska defects, Chakotay even turns to Tuvok for guidance, asking if the Vulcan thinks it is a flaw in his personality which allows him to be so easily fooled.
Playing By The Rules
When Chakotay and his crew first join Voyager in the Delta Quadrant, he clearly dislikes Tom Paris. The two apparently had dealings during Paris' brief and disastrous career in the Maquis. Chakotay suspects Paris of selling Maquis secrets to the Federation for an early release from prison, and is revolted by his betrayal.
Chakotay is a man of honour and principles, even if the principals he follows aren't accepted by a majority of the people around him now. The Maquis may have a different way of doing things, but a good leader is a good leader in any situation, and Captain Kathryn Janeway of the Voyager recognises this. When she has to appoint a new First Officer, she turns to the man who can best unite the two disparate crews.
Chakotay certainly has the leadership abilities and experience to fulfill his role. He seems to shed his resentment of Starfleet rules and regulations with surprising ease, and sees the logic of Federation procedures much more easily than some of his fellow Maquis. When Seska breaks into the food stores to make his favourite mushroom soup, Chakotay isn't amused by her "Maquis operation", and disciplines her. On the other hand, when she joins a Kazon sect and is a danger to the entire Voyager crew, Chakotay takes off after her himself to solve the problem in his own style.
Lost in the unexplored Delta Quadrant, Chakotay is willing to put aside his differences with a government thousands of light years away. Janeway is a Captain he can respect and follow, and their mission to find a way home is one he can believe in. Above all, the Delta Quadrant provides an endless voyage of discovery, enough to satisfy even Chakotay's curiosity.
Members of Chakotay's Maquis crew who were aboard the "Liberty" when it was swept into the DQ include B'Elanna Torres, Lon Suder, Kurt Bendera, Kenneth Dalby, Mariah Henley, Ayala, Hogan, Jackson, Seska, Gerron, Jarvin and Chell.
Side Note: Other notable Starfleet defectors to the MaquisMany Starfleet officers recognise that the Cardassians have not honoured the treaty which created the Demilitarised Zone and feel that the Federation's response has been inadequate. When these officers become directly involved with a war in which former Federation colonists are defending their homes and the lives of their families, they often turn a blind eye to illegal arms sales or even decide to leave Starfleet and join the Maquis - for example:
Commander Calvin Hudson, Lieutenant Ro Laren, Thomas Riker, Tom Paris, Lieutenant Commander Michael Eddington.
Information gathered and transcribed from "The Official Star Trek Fact Files" and Jeri Taylor's, "Pathways".
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