This is an alternate universe story about what it might have been like if the Starfleet and Maquis crews had not merged as cleanly as they did.
Spoilers: Since this is AU, it does mention events of episodes, but not necessarily exactly what happened as written by TPTB. Tom Paris's history is taken from the show, and I made up what we were never told.
Warnings: Descriptions of injuries sustained from violent acts, language, a none to clean mutiny.
Yeah, I own them. I own them all. Not. Broke, not profiting. All lawyers can now chill.
No one could possibly have expected a small Federation vessel, prepared only for a short journey, to last even a year stranded in a hostile foreign quadrant. The chances of survival diminish even more when the crew of said vessel is made up half by unrefined terrorists, half by the people sent to capture them, and by one man who has managed to betray both sides. And although the ship's survival is remarkable, the relation of its unlikely shipmates is as predictable as former prey's civility to its one-time predator. That is to say, just to the left of unstable peace and just to the right of a continuous brawl. The prospering ship is a stark contrast to it's failing crew, where insubordination is always a precedent to a sudden outburst of fury. But then, metal bulkheads are easier to fix than cracked hearts and lonely lives. Everyone on Voyager reacts to their own pain by inflicting some on others, whomever they blame for the vast distance between them and home. The Starfleet crew blames the Maquis. The Maquis blame Starfleet. In sickbay, there are two medical assistants, one Maquis and one Starfleet. They treat their respective colleagues, and one has yet to see either one cross ranks and treat someone with insignia different from their own. It is truly a wonder how Voyager has lived with out a full-blown mutiny, by either the Starfleet crew or Maquis, trying to get rid of the other. There is a rare existence of agreement between the two on one person: Tom Paris is responsible for all of Voyager's troubles.
With the exception of a few in the know people, not much is known or even cared about Tom Paris, beyond that he was once a Starfleet Cadet, kicked out of the academy for a nasty shuttle accident in which he claimed responsibility all but too late. Afterwards, he joined the Maquis as a mercenary pilot, but was captured by the Federation almost immediately. He was convicted of a variety of crimes relating to Maquis activities. After reading a small amount of Federation law, it becomes apparent that a Maquis crime conviction is a legal game of dominoes, particularly for a Federation citizen and former Starfleet cadet. Once convicted of being a Maquis, it is almost certain that one will also be convicted of treason, terrorism, and trafficking arms and contraband. It seems a tad unfair to one without the hatred for the Maquis contained by most Starfleet courts, who cannot question the legitimacy of such laws that allow them to lock up Maquis by the hundred. Tom Paris, surely, did question the laws that sent him to Auckland Penitentiary for eleven years and seven months, in addition to five months of time served while he was awaiting trial and then sentencing. Twelve years is a long time out of a young man's life. Which is probably why he said yes.
Yes to Captain Kathryn Janeway's request for a qualified guide to lead her to the Maquis, to Tom's former cell leader, Chakotay. And if he did, he'd have her respected words at the hearing the following year, where he might be released eight year earlier than his sentence read. Who would say no? He didn't. He lead her to the big Maquis' stomping grounds, and Voyager was tossed through space to land on the other side, far too quickly, far too great a distance from the Bad Lands, with far too many casualties sustained from the bumpy ride. It wasn't Tom's fault. The deaths of Voyager's first officer, chief engineer, pilot, and entire medical staff were not his fault. He did what he was asked; he led them to the Maquis. He fulfilled his end of the bargain, on the other side of the Galaxy.
And wished like hell he hadn't, considering the consequences. When the Maquis ship was destroyed, his former comrades boarded Voyager. "Traitor!" His one-time associates hissed at him. He never expected to survive past that first tension-filled meeting on Voyager's bridge. The first week was pretty safe for Tom; the discovery of Janeway's Vulcan security officer as a spy on Chakotay's ship turned the Maquis' attention elsewhere. The Maquis had someone else to hate and plot to assassinate for a month. The addition to the crew of the friendly Delpha Quadrant native Neelix, who had attempted to save but ultimately lost his mate, a elfish telepath named Kes, as well as the controversial Maquis crew assignments, and the Emergency Medical Holograph's less than stellar attitude upon activation made the first month too busy for Tom to know what would happen in later months. Tom feared Chakotay's appointment as first officer, and he envied Batehearts's appointment as pilot.
Whatever Captain Janeway's intentions for Tom were, she kept them to herself, for she left him unoccupied for the first 6 months of the journey. It was then that the Maquis began taking their revenge. Tom's various Federation enemies followed suit. From that moment on Tom Paris has been treated for the fracture of every major bone in his body. Treated for internal organ damage, cranial hemorrhaging, and even one most unfortunate case of bowel perforation, as well as other severe damage in that area. That never happened again, someone in power ordered that particular kind of abuse to cease. Possibly Commander Chakotay, who spent time in Cardassian slave camps, and saw many assault victims. Commander Chakotay could end half of Tom's suffering with one order, and although he's certainly lessened it, he is still responsible for the broken ribs Tom received a week ago, having never condemned it. However insubordinate and obnoxious the Maquis are to Federation officers, they are always obedient to Chakotay. Maquis captains have always been practitioners of corporal punishment to keep their crews in line, many suspect it still goes on behind Tuvok's vigilante surveillance of the Maquis. It's sad and sickening that one can tell which side attacked Tom by the wound. The Maquis are creative and resourceful; they could make a weapon out of anything. They have to; Lt. Tuvok strictly regulates weapon replication, and is especially careful about keeping phasers out of Maquis hands. Starfleet crewmembers can easily get weapons, which is probably why Tom limps to sickbay singed and blistered so many times. Tom's used his programming skills to prevent the EMH from reporting his injuries to the Captain, before he had tried seeking no medical attention whatsoever and using a regenerator that didn't even begin to treat most of his injuries. While most of the crew decidedly wanted to avoid encounters with hostile aliens, Tom enjoyed Red Alert because it meant everyone not on duty was in their quarters, so Tom wouldn't get shoved as he walked down the corridor, or receive a warning glare that indicates he can expect a lot more than shove later. Stress tends to put the crew on edge, but atleast they're too busy to bother him at the moment. Over the months, the fights had been less brutal and more time passed in between. Tom didn't know if Janeway had found out or if Chakotay was helping him out, or if he'd finally lost the interest of his tormentors. He certainly was unaware of the Maquis' side project, which was a great distraction. He wasn't about to experiment, but rather enjoy not having fresh bruises everyday.
The second year of the journey he'd been assigned to the botanical garden. To get to the converted cargo bay, he had to pass the shuttle bay on a daily basis. It was really only a matter of time before it occurred to him that his means of escape were right outside the door. And only a matter of time, three weeks, until he got enough courage to turn into the wrong room. What was a complete accident was that Chakotay was in the Shuttle Bay when he came to check out which shuttle he would use for his flight. Tom entered the Shuttle Bay with the same determined pace he'd been striding through the ship with. No variation his steps communicated he was intent on a destination. Or atleast he was until he saw Chakotay. He tried to backtrack through the door, but it slid shut with an audible hiss, enough to get Chakotay's attention.
Oh Shit, Tom thought.
"Paris."
"Oh, Chakotay." Tom hastily covered the stream of mental expletives with a tone of indifference in his greeting. With the Maquis he usually reverted to a tone of arrogance that got him attacked, but not with Chakotay. Chakotay was too damn big for him deliberately provoke, atleast when he was not in the mood to get pounded. Tom had a few inches on the man, but Chakotay had what really counted: mass. Besides, Chakotay had never directly hurt Tom in the year they'd been on the same ship. Yelled at him, berated him, certainly not stopped other Maquis from hurting him, but never personally taken a hand or anything else to Tom. Why stop a good thing when it's on a roll?
"Walked into the wrong room, can you believe it? I meant to go to the garden," Tom explained, already with his back to Chakotay.
"Wait, Paris. I was meaning to talk to you."
How wonderful, Tom thought, marveling at his ability to be sarcastic within his own head.
Tom turned half way around.
"About what?"
"The vegetables you gave Neelix last week. They gave half the crew food poisoning."
Good. That's what they were supposed to do. I wouldn't have gone to all that trouble of injecting them with Rajivian poison if it didn't have an effect, Tom thought bitterly.
"Really? " I scanned them before I gave them to Neelix, he must have cooked them wrong or something."
"The doctor found traces of Rajivian poison in the afflicted crew members."
"Well, we did receive the seeds from one of the planets in the Rajivia Empire. The Rajivian people might not be as well intentioned as they appeared. But I wouldn't know, remember? I'm not allowed off the ship. You'd have to ask the away team that traded for the seeds."
"I was on the away team. When we scanned the seeds there was nothing to indicate poison."
"Maybe you made a mistake."
"I don't make mistakes, not ones that endanger this ship."
"Maybe you did, this once."
With that, Paris turned completely and left as he had entered. He strode down the corridor, into the converted cargo bay of plants and topsoil. I hope he puked for a week, he thought, dropping to his knees next to the tomato bush. He ripped out some offending weeds from its base. I am a pilot, not a damned gardener. I'll poison the entire crew if I have to. Hell, I'd poison the entire crew just for kicks. His hands began to bloody from the sharp stems, but he didn't stop.
While Paris steamed, Chakotay stared at the door from which he had departed. B'Elanna Torres stuck her lightly ridged head out from a shuttle hatch.
"He deliberately did something to those vegetables, didn't he?"
Chakotay turned around, as B'Elanna climbed out of the shuttle and reclined against it.
"Yes," Chakotay strolled closer. "And he's probably going to do it again."
"Shouldn't we do something?" B'Elanna approached her commanding officer, noting he looked more amused than enraged.
"No."
"Why?"
"Because, if it happens again, Janeway will figure it out. She'll take care of it."
B'Elanna's voice took on an edge. "Since when do we leave things to those Starfleet fucks? Especially when we can handle it so much better."
Chakotay's voice took on an edge of it's own, far more dangerous than anything Torres could produce. She was instantly cowed.
"Tom Paris is the least of our problems, B'Elanna. Focus on the big not the small. Understand?"
"Yes, sir. But I don't understand how that applies in this particular situation," B'Elanna continued, despite the danger she knew could come of questioning Chakotay. "Sir," she quickly added.
Chakotay sighed. He knew the hatred for Tom Paris harbored by his crew was strong. He didn't share it as strongly as he once had. He didn't have the God damn time. Why the crew continued to focus on Paris, rather than Tuvok, Janeway, or any of the others equally responsible, was beyond him. Not that he liked Paris, the arrogant--
"Sir?" B'Elanna interrupted his thoughts.
Chakotay looked at B'Elanna and sighed again. The woman was irritated at his delayed response, and he had lost his own irritation with her pressing questions.
"If Paris gives the ship indigestion, it's not going to interfere with our plans. It might even help create a distraction. If you take action, Janeway or Tuvok will keep an extra eye on us. That's not what we need now. It's not worth it, B'Elanna. When we're done, you can do whatever you like to Paris, if he's still on the ship," Chakotay pacified, suddenly very tired.
"Still on the ship? You'd let him leave?" B'Elanna was incredulous.
Chakotay met B'Elanna's wide eyes with his own hard stare, "The coming weeks aren't going to be organized, B'Elanna. If it works, it's not going to be clean. They aren't going to line up so we can pick and choose who stays and who goes."
B'Elanna nodded slowly. She returned to the shuttle, and Chakotay left the bay for a nap in his quarters. It was apparent to B'Elanna, who knew him so well, although he hid it carefully from everyone else, that the man was exhausted. She didn't blame him. Leading a mutiny wasn't exactly restful. The Maquis had been plotting this for over six months. They'd finally reached the stage where it wasn't just a detailed plan for the future, but a daily routine where nearly everything they did was in preparation for the big event. B'Elanna wasn't repairing the shuttle; she was setting everything on board, the replicators, engines, life-support, sensors, warp, and other vital components to endure a journey of decades. As much as some of them deserved it, the Maquis weren't just abandoning the Federation's people in the middle of space. They would be given the shuttles to continue home on, or they could choose to make a home on the inhabitable planet that Voyager's course would bring them to in a matter of weeks. But they could not stay on Voyager. Not anymore.