Episode 2, Season 1-Parallax
This is the first episode in which we get to see Chakotay and Janeway working together as First Officer and Captain, and it very much sets them up for success. The main conflict is whether or not B'Elanna is suited to be Chief Engineer. Janeway is surprised when he suggests her, and then when they're on the bridge and need help from Engineering, Chakotay calls B'Elanna first. Janeway is clearly scandalized, and calls to her Starfleet engineer instead, putting him in charge. She and Chakotay go into her ready room and they have an argument about whether the Maquis can or should have any command positions. It gets fairly heated, and towards the end, he says, a little more gently and with a slight sadness that he's trying to help her, and is sorry that she can't see that. I think that though he cares about his people and wants to take care of them, helping Janeway integrate them and run a successful ship is one of his top priorities. Despite the fact that Janeway is skeptical of B'Elanna, I think she realizes that Chakotay has her best interests at heart.
Unfortunately, when she tries to talk to B'Elanna later and get to know her, B'Elanna's temper flares, and it goes poorly. Still, Janeway agrees to allow B'Elanna to be in the meeting later in the episode in which they're discussing how to escape the black hole. This time, Janeway gets to witness B'Elanna's brilliance, and she doesn't ignore it. Right as everyone is leaving the ready room, Chakotay glances back at Janeway to gauge her feelings. She smiles.
Which makes him give her his soft smile, one that just grows softer over time
After Janeway makes B'Elanna Chief Engineer, she watches her from the deck above as B'Elanna makes her amends with Carey, the Starfleet Engineer who would have been Chief Engineer if it wasn't for her. Chakotay joins Janeway, asking, a little guardedly, if Janeway is checking up on B'Elanna. Janeway simply says that she's observing, and that B'Elanna will definitely have to face some opposition:
Their connection thus deepened, Chakotay asks if she would have served under him if they were on the Maquis ship. She grins and says that as Captain, she gets to keep some things to herself. And they share the first of what will be many looks of fond amusement:
As always, additions or disagreements are welcome!