Set after the episode Investigations (where Tom has been given an undercover mission to find the traitor on Voyager)
"Come in." Chakotay said. He was in a foul mood. After nearly 2 years in the Delta Quadrant, Kathryn Janeway, whom he'd considered a friend as well as a colleague, hadn't trusted him enough to put him in the loop regarding the plan concocted by her, Tom Paris, and Tuvok. Janeway colluding with two traitors...Janeway had apologised but he didn't get the feeling she would have done it differently, and it bothered him. A lot.
The person to enter his quarters was one of the last people he wanted to see at that moment.
"Paris." He said, coolly. Tom waited for the door behind him to close.
"I came to apologise." he said, and his voice included all of the sincerity, regret, and self-reproach that it should - but now he knew more than anyone just how good an actor Tom was. His fluency in lying shouldn't have come as a surprise to Chakotay, but it still had.
"For what?" Chakotay said. He knew how he had to play this. He was angry now, but his reason told him that it wasn't really Tom's fault - he'd just been the agent in the plan, he hadn't made the decision to exclude Chakotay.
Tom sighed. "For... everything. For hitting you. For undermining you in front of the crew..."
"You were just following the script Lieutenant, following orders. You didn't do anything wrong and you have nothing to apologise for. Was that all?"
Tom stared at him with an unreadable expression. There was an awkward pause before Tom finally said.
"Chakotay, I was following orders to be a complete asshole to you, so I owe you an apology. I also should have insisted that you were in on it. I'm sorry."
Chakotay felt his anger dissipating slightly, but before he could say anything, Tom continued.
"I also came to say Thank You."
"For what?"
"Not believing it too quickly." Tom said, with a wry smile. But Chakotay frowned.
Chakotay looked at him, saw the Tom he'd started to see before this plot started, the one who was trying so hard to do the right thing, to make up for past mistakes. The Tom who was so hard on himself, and so often forgave everybody except himself. He let go of his resentment and put his anger at Kathryn to one side to focus on the pilot.
"Did you think I would?"
Tom shrugged. "I haven't given you much reason to-"
"To what Tom? See you differently from the alcoholic hustler I recruited in Marseille? Of course you have." Chakotay sighed and shook his head. Tom's sincerity had won him over despite his bad mood, and he saw it all from the pilot's point of view as well as just his own. "In the last two years on Voyager you have shown yourself to have courage, compassion, and decency. You have proved yourself time and again"
Tom looked genuinely stunned by the words.
"Sit down, please" he gestured towards the sofa.
"Do I wish I'd been included in the plan? Yes. I do, and I've spoken to the Captain about my disappointment with her decision. But your actions were selfless and resourceful and deserve recognition."
Tom shifted uncomfortably, looked like he was waiting for the penny to drop, and Chakotay realised this was probably the first time he'd ever praised him.
"You put yourself at risk, in more ways than one. How much backlash did you get from the crew for your behaviour?"
Tom shrugged. "Nothing I can't handle."
"It's still going on?"
"They'll get bored eventually." Tom said indifferently.
Chakotay looked at him.
"After all the work you put into building good relationships on Voyager, you risked it all on this mission. All the hard won respect - now you have to build it up again. I've seen the way some of the crew were behaving around you Tom."
Actually, Chakotay had had to order some of his former crew to keep their hands off the young pilot. No matter how angry he may have been, he refused to let anyone touch him. Some of them had implied that there had been a few attacks in the early days...the thought of which disturbed him. Tom had never said anything, he had covered for them. He knew it would have risked the stability of the crew back then...but that didn't make it any easier for Chakotay to accept.
"Neelix wants to interview me in an hour to explain... I'm hoping it will help somewhat."
"If anyone tries anything, I want to be the first to know. I meant everything I said back there about coming to me with anything that's bothering you."
Tom sighed and laughed slightly. "One step forward and two steps back, huh?"
"You're not back to square one Tom, people know you now. You just have to remind them of what they already know"
"I feel like I've been hustling pool in Marseille. You build up this story... then right at the end turn it all around, and it's supposed to feel like some kind of victory but..." he shook his head. "Most of the time it just ends with everyone in the room hating your guts and trying to prove it."
"Back then you did it for money. This time you did it for Voyager. Having said which, if you try to hustle me again I might not be so forgiving." Chakotay said drily.
Tom looked sheepish. "I won't. I'd better get going for Neelix's report..."
He got up to go and they walked to the door.
"Tom, thank you. It means a lot to me that you chose to come here this evening and say what you did."
Tom smiled at him "Least I could do. Good night Commander."
"Good night."
Chakotay stared at the closed door after Tom had left. He recognised the look on Tom's face from times when the Captain had praised him- the look that said Tom would do anything to live up to that faith in him.
He'd never seen Tom look at him like that before, he'd only seen caution, cynicism, supicion. He realised now why Kathryn felt so protective of Tom. There was something about winning the trust of Tom Paris that felt like a greater victory than the whole of his former maquis crew put together.