Chakotay's early life was not an altogether happy one; his father was a traditionalist who tried to educate his children in the ways and beliefs of their ancestors. Chakotay rejected those teachings, and this was a source of some friction between the two. Later he was to come to appreciate what his father had been trying to teach him, and Chakotay has tried to combine the best elements of the twenty fourth century with the traditions of his tribe. At age eighteen Chakotay joined Starfleet Academy, and graduated successfully in 2354. 
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His Starfleet career was a distinguished one, but when the Federation signed a treaty ceding considerable territory to the Cardassians , Chakotay resigned his commission and joined the Maquis to defend his home colony from Cardassian occupation. In 2371, Chakotay was commanding a Maquis vessel near the Badlands when his ship was attacked by a Cardassian warship. He managed to lose the Cardassians in the plasma storms, but his ship was dragged into the Delta Quadrant by the Caretaker as part of that entities experimental breeding project.  Chakotay formed an alliance with Captain Janeway of the USS Voyager in order to try and find a way home. When his ship was destroyed by the Kazon, Chakotay was appointed First Officer of Voyager by Captain Janeway.  He has served in this post ever since. Chakotay has acted as something of a counterbalance to Janeway's runaway ego on Voyager, and is often the ship's main voice of reason.  This has led to direct opposition on at least two occasions; the first came when Janeway allied with the Borg against Species 8472. When Janeway was injured she ordered Chakotay to make the alliance work in order to allow Voyager to cross Borg space. Nevertheless, once she was unconscious he dissolved the alliance and struck out on his own.  On the second occasion Janeway attempted to force information from a member of the USS Equinox's crew by allowing hostile aliens to attack him. Chakotay disobeyed direct orders in order to protect the man, and later admitted that he had considered attempting to remove her from command. During 2377 Chakotay and Seven of Nine began to become attracted towards one another, and in the latter part of the year they pursued a romantic relationship.