Tom met Chakotay when he joined the Maquis after getting kicked out of Starfleet. Tom had been involved in a fatal accident that cost the lives of three of his fellow cadets. Tom lied on the report but later admitted that it was pilot error. He was cashered out of Starfleet not for the pilot error but for falsifying the report. Chakotay was a leader within the Maquis and sent Tom on his first mission. As fate would have it, Tom was caught on his first time out which landed him a prison sentence in the New Zealand penal colony. It was here that Captain Janeway found him and recruited him to help her find a Maquis ship that had gone missing in the Badlands, a dangerous area of space, a ship that just happened to have been flown by Chakotay and his crew. Whilst acting as an observer aboard Voyager, a new Federation class of ship, Tom found himself flung to the other side of the Universe seventy thousand light years from home. And stuck on board the same ship as Chakotay and the Maquis crew after their ship is eventually destroyed.
It is here that the two of them begin to get to know each other in a way that they didn't back when Tom joined the Maquis. Their relationship didn't exactly get off to a good footing and the two of them 'didn't exactly get along' (Janeway - The Caretaker). Through the series we can see them becoming collegues and maybe even friends, though in the world of C/P we see them becoming a lot more, of course!
The whole relationship in the pilot epsiode is geared up towards an interesting relationship between the two men, in relation to their shared history and pasts. There was a lot of tension between them, that should have in my eyes resulted in a few more fights and arguments or even disagreements than what was actually shown in canon. When they first met in the Maquis we are lead to understand that they did not get on and that Chakotay considered Tom a mercenary. This has transended to the C/P world where this history of tension has been transmuted into sexual tension, something which when you examine their past history is very believable.
To know more about our
favorite couple go to the C/P history section