Chakotay is one of the leaders of the Maquis, a group of displaced or unallied people of many cultures who are fighting against the Klingon Empire. At the time of Mirrors, he is a Captain of a Maquis ship, roughly half the size of 'Voyager', with approximately seventy crewmembers on board.
As Captain, Chakotay rules with an iron hand. His word is law aboard his ship, as Tom Paris finds out when he is 'recruited' aboard the Maquis ship by B'Elanna Torres. Chakotay takes Tom as a lover shortly after he arrives on board - not only because he wants Tom, but because he wants to save Tom from the elaborate sexual hazing that he would undergo from the other Maquis.
Part of Chakotay's 'compassion' for Tom is explained by the fact that he was imprisoned and raped by the Klingons in one of their labour camps. It is one of the events in his life that has shaped who he is to this day; one of the others was the accident that destroyed a previous Maquis ship, and cost his half-brother, Julian "Jules" Bashir, his eyesight. Although Jules himself was flying when the accident occurred, Chakotay felt he was responsible because he was in command of the ship and should have removed Jules from duty.
Although Chakotay has healthy sexual appetites (among his former lovers are Torres and Tuvok), he is confused by his feelings for Tom, and as a result pushes the young man away, feeling guilty that Tom was only sleeping with him under duress. Tom, in turn, believes that Chakotay is in love with Tuvok, and makes no move to come between the two old friends when Tuvok returns to the Maquis after his undercover mission on 'Voyager'.
Chakotay is friends with Jules' Cardassian lover, Elim Garak, although he doesn't completely trust the Cardassian Underground of which Elim and Jules are both working members. He is proven right when the Obsidian Order moves in and removes the Cardassian Nationals from Hutet and other Cardassian cities involved in the Underground. After this happens, he retrieves Jules and brings him back to his 'new' ship, the 'Phoenix' (formerly known as 'Voyager', under the command of Kathryn Janeway).
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