In his first year at Starfleet Academy, Chakotay trained as a pilot over Earth's North American continent, and then spent two months on Venus learning how to handle atmospheric storms, and later learned to dodge asteroids in that system's asteroid belt [Future's End].
After leaving Starfleet Academy, Chakotay was a member of the Starfleet mission which made first contact with the Tarkannans [Innocence].
According to his conversation with Valerie Archer on their date in [In the Flesh], on one occasion he was beamed somewhere wearing nothing but his combadge.
Chakotay abandoned Starfleet to join the Maquis and defend his homeworld against Cardassian attacks. He was recruited into the Maquis by Sveta, who in 2374 sent him a letter transmitted by Starfleet through the Hirogen relay network to inform him that almost all the remaining Maquis had been massacred [#83 Hunters]. Chakotay rose to command rank in the Maquis.
Commander of Maquis ship [#1 and #2 Caretaker]
He commanded the Maquis vessel which was pursued by the Cardassian commander Gul Evek into the Badlands in 2371; it was on this occasion that his ship, and later Voyager, was catapulted to the Delta Quadrant.
THE HISTORIC MEETING OF CHAKOTAY (MAQUIS) AND JANEWAY (STARFLEET)
After he and his crew are kidnapped by the Caretaker then returned to their ship, Chakotay is contacted by Janeway. One of her crewmembers, Ensign Kim, is missing and she wonders if he has been sent to Chakotay's ship. Chakotay asks how she knows his name and she replies that they came looking for them. Chakotay says he is missing a crewmember too, his engineer Torres. Janeway says their problem is the same and suggests they work together. Chakotay consults Tuvok who agrees by nodding his head. Chakotay says he and two others will beam to Voyager.
Chakotay, Tuvok and another Maquis member beam aboard Voyager. They arrive armed and ready. Janeway tells them that weapons are not needed here.
Then she greets Tuvok, whose undercover role is revealed. Chakotay is grim but doesn't get angry until he sees that Paris is involved.
"At least the Vulcan was doing his duty as a Starfleet officer, but you, you betrayed us for what - freedom from prison, latinum? What was your price this time?!" Janeway tells Chakotay she expects him to grant the same respect to a member of her crew as he would expect her to give one of his.
The reconciliation process between Chakotay and Paris begins during their mission to the Ocampa homeworld to rescue the missing crewmembers B'Elanna Torres (Maquis) and Ensign Harry Kim (Starfleet). Chakotay breaks his leg trying to escape up collapsing stairs to the planet surface. Paris insists on rescuing him, because it's a tradition among Chakotay's people that if does so, Chakotay's life would belong to him. Chakotay replies, with some humour, "Wrong tribe." But Paris doesn't believe him and pulls Chakotay clear just as the stairway collapses and plunges down the shaft.
Chakotay sacrificed his ship to destroy a Kazon-Ogla one that was attacking them. After Janeway destroyed the Caretaker's Array to prevent the Kazon appropriating its technology and abusing it to gain power in the region, Chakotay accepted Captain Kathryn Janeway's invitation to join her crew - they agreed it would be one crew, a Starfleet crew. Chakotay himself became her first officer with the rank of Commander as his predecessor Lt. Commander Cavit had been killed by the displacement wave. He retained his Maquis collar badge of rank. [#1 and #2 Caretaker].
Chakotay's Starfleet service number is 47 alpha 612. He resigned his commission on 3rd March 2368 in person at Starfleet Headquarters, San Francisco, Earth, to Admiral Nmembi (the Admiral taught Tactical Analysis at Starfleet Academy). [#98 In the Flesh]
Aboard USS Voyager, Chakotay is the next senior officer after Captain Janeway. His post on the bridge is in the command centre, and his chair is adjacent to the captain's chair, on her left. As First Officer, he has charge of the personnel duty rosters, as noted in several episodes including [#73 Revulsion], [#125 Alice] and [#171 and #172 Endgame].
Chakotay enters the bridge. (pop-up window) [#157 Shattered]
While Janeway has clearance level 10, he does not have Level 9 authorisation or above because in [#120 and #121 Equinox] when he presses buttons on the LCARS wall panel to try and raise the forcefield round the cargo bay in which Noah Lessing is a prisoner, the computer responds: "Level 9 authorisation required." [#89 The Omega Directive] establishes that Janeway has clearance level 10, which indicates that clearance levels ascend in the numerical order 1 (lowest) to 10 (highest) (in which context can be read the fact that USS Prometheus' computer informs the Doctor that tactical data on the ship is restricted to Level 4 clearance and above [#82 Message in a Bottle]). Janeway has clearance level 10 in order to be able to access the highly confidential data which Starfleet holds on the Omega molecule.
Chakotay's professional and personal relationship with his captain are often mixed together. For details of the more personal side, beam here.
DISAGREEMENT WITH THE CAPTAIN
Chakotay is not afraid to disagree with the Captain's decisions but he does consider carefully whether to do so. He also informed her early on, in [#3 Parallax], that he would not be her token Maquis officer. His opinions are freely expressed, whether in support or in disagreement, at his weekly dinners with the Captain.
Right: Janeway brings from the replicator the meal she has prepared for Chakotay. You can see that her glass is half-full with a red liquid, possibly red wine, but that Chakotay's glass contains water.
[#129 The Voyager Conspiracy]
Chakotay suggests a Kazon alliance [#30 Alliances]
Following a series of damaging raids by Kazon ships, Chakotay told Janeway that he would not be her "token Maquis officer" and questioned whether Starfleet principles were appropriate in the Delta Quadrant. "Maybe we should be thinking more like the Maquis." [#30 Alliances]
In [Scorpion, Part One] Janeway told Chakotay: "Three years ago I didn't even know your name. Today, I can't imagine a day without you."
Chakotay's relationship with Janeway came under strain in [#68 and #69 Scorpion] when he disagreed with her decision to form an alliance with the Borg against Species 8472.
[Scorpion]
To illustrate his objection to a Borg alliance Chakotay tells the parable of the scorpion: "A scorpion was walking along the bank of a river, wondering how to get to the other side. Suddenly he saw a fox. He asked the fox to take him on his back across the river. The fox said, 'No, if I do that you'll sting me and I'll drown.' The scorpion assured him, 'If I did that we'd both drown.' So the fox thought about it, finally agreed. So the scorpion climbed up on his back and the fox began to swim. But halfway across the river the scorpion stung him. As the poison filled his veins, the fox turned to the scorpion, said 'Why did you do that? Now you'll drown too.' 'I couldn't help it,' said the scorpion, 'it's my nature.'
Janeway says she's "not trying to change the nature of the beast". She calls the Doctor her "guarantee" [he alone possesses the nanoprobe knowledge, separate from the ship's computers, and his program can be erased]. "We just need the courage to see this through to the end," she says.
Chakotay replies, "There are other kinds of courage, like the courage to accept that there are some situations beyond your control. Not every problem has an immediate solution." When Janeway says that maybe assimilation by the Borg of Species 8472 would be doing a favour, Chakotay says he knows she doesn't believe that. "I think you're struggling to justify your plan, because your desire to get this crew home is blinding you to other options. I know you, Kathryn. Sometimes you don't know when to step back."
But Janeway overrules him. He says that he'll follow her orders but he doesn't have to agree with them.
[Equinox]
Chakotay and Janeway clashed again in [#120 and #121 Equinox].
Janeway: "We've had our disagreements, Chakotay, but you've never openly opposed me."
Chakotay: "You almost killed that man today."
Janeway: "It was a calculated risk and I took it."
Chakotay: "It was a bad call."
Janeway: "I'll note your objection in my log."
Chakotay: "I don't give a damn about your log! This isn't about rules and regulations. It's about right and wrong. And I'm warning you: I won't let you cross that line again."
Janeway: "Well then you leave me no choice. You're hereby relieved of duty until further notice."
Chakotay: "What's happened to you, Kathryn?"
Janeway: "I was about to ask you the same question."