Commander Chakotay's combination of Maquis experience and Starfleet training makes him an unusual First Officer, but his tendency to view the people under him as friends rather than subordinates can sometimes conflict with his duty.
Chakotay is far from being a typical Satrfleet second-in-command, but Captain Janeway considers him to be the ideal replacement for her deceased First Officer aboard the U.S.S. Voyager NCC-74656. He is a quietly authoritive man whose experience with the rough-and-tumble Maquis rebels and the strict rules of Starfleet combine to form a leader of unique attributes.
When Chakotay gives orders, he expects them to be followed; his trust in those around him is the basis of his command style. He is extremely loyal to crew serving under him, and considers himself responsible for their actions. As a Maquis leader, Chakotay was accustomed to throwing a few punches to make his point, and on occassion, he has used this method on 'Voyager' to give troublesome, undisciplined crew members a short, sharp reminder of the differences between Starfleet and Maquis protocol. But leading a band of rebels presented very different problems, and Chakotay is quick to understand that things cannot work this way on an essentially Starfleet vessel, lost a long way from home.
Just because someone happened to be in the Maquis, or even in prison, before joining 'Voyager's' crew is not, in Chakotay's opinion any reason to ignore Starfleet rules now. Unaware that Lt. Tom Paris' behavior is part of a ruse to expose a Kazon collaborator on the ship, Chakotay reprimands him for constantly being late for his duty shifts, and for his unkempt uniform. As First Officer, Chakotay feels crew discipline is important, and he is not afraid to let those who step out of line know how he feels. On the other hand, the intuitive style he owes more to the Maquis, serves 'Voyager' well in handling the many surprises the crew encounters in the Delta Quadrant
Different Outlook
Chakotay has the ability to see patterns and solutions where others don't, possibly because of his spiritual nature and his belief that everything in the Universe is interconnected; he is used to letting his feelings, rather than Starfleet rule books and protocol, guide his command decisions.
But effective as he is in giving commands and overseeing the welfare of the crew, Chakotay isn't necessarily as good at following orders himself. He and Captain Janeway have an interesting relationship, one built on mutual respect and admiration, though at times it's something much deeper than simple friendship. For Janeway, cut off from Starfleet Command with only her conscience and her officers to advise her, Chakotay's quiet friendship and support is vitally important. For the most part, he abides by her decisions and implements them with little question, but when he does disagree, he makes sure she knows it, such as when she wants an alliance with the Borg to fight Species 8472. He thinks the proposed deal is a fatal mistake, and when Janeway is injured and he has command of the ship, he does not hesitate to break off the alliance - decompressing a cargo bay and spacing a group of Borg when they become a threat. When Janeway recovers, she is disappointed with his decision, but respects him enough not to let it seriously affect their relationship.
Unlike a typical Starfleet officer, who usually maintains a suitable distance from his crew, Chakotay counts several 'Voyager' officers as friends. Even Janway acknowledges that her First Officer is closer to the crew than she is. But this closeness also means that he takes betrayals more personally, as though the blow has been dealt to him as much as the organisation he represents. Chakotay questions his ability to command when he learns that, while in his Maquis cell, Tuvok and Seska - both of whom he trusted implicitly - were spying on the Maquis for Starfleet and the Cardassians respectively. But in most cases his closeness to the crew serves him well; on such a small ship - alone in a strange and dangerous area of space, this can only be an advantage.
Bringing together his spiritual beliefs with his life on 'Voyager', Chakotay creates a flexible command style that is particularly useful in guiding the crew and supporting the Captain in her mission to get everyone home.
Captain Chakotay
In an alternate future experienced by Kes, Chakotay becomes Captain of 'Voyager' following the death of Captain Janeway at the hands of the Krenim. Assuming command during the battle, Chakotay manages to convey compassion for his crew, while at the same time demanding they continue to handle the crisis to the very best of their abilities; his clear head ensures that the tragedy does not claim more lives. As time passes, Chakotay becomes a somewhat more formal man than the one the crew have known, but this is to be expected as he keeps his distance, in the way that Captaincy demands.
Information gathered and transcribed from "The Official Star Trek Fact Files" and 'Star Trek: Voyager' episodes.
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