The Missing Scenes Series

Episode 1x01 - Caretaker

Disclaimer: All things Star Trek belong to Paramount and CBS. I'm just writing the bits that TPTB seemed to have missed.

Note: These are the missing scenes at the end of Caretaker, between when Captain Janeway destroys the Caretaker's array and when she tells Tom that the Maquis will be joining her crew.

Captain Janeway departed the bridge at the end of her shift, making her way back to her quarters without really seeing the trip. The phaser she wore rattled slightly in its holster, reminding her that it was still there, and of the necessity for it. Things were a mess. Nothing in all of her Starfleet training could have prepared her for the situation she now found herself in. Ships that were lost were in the habit of being lost forever. As she walked, she idly wondered if there were any other ships that might have already spent years making their way back to the Alpha Quadrant.

Before she even realized it she was in her quarters, a strange place that she hadn't really spent enough time in to get used to yet. There were only a few things in it that weren't standard starship issue – practical things that she thought she would need over the next few weeks. There were no picture frames, no books, nothing really decorative. Mark had suggested that she take a couple things on board to make her home away from home more comfortable, but she assured him that she would continue to take things here and there every time Voyager returned to Earth.

Earth…

For the first time since destroying the Caretaker's array, the enormity of what had happened started to hit her. Mark was gone. Molly was gone. Her mother, her sister, her friends, her mentors…all gone. Her life seemed to be travelling on a perfectly normal plain when they left Deep Space Nine the week before. And now, completely against her will, that life was over. Someone may as well have held a phaser to her chest and pulled the trigger.

The very thought of it reminded her of her sidearm, which she pulled out and held up in the dim light to look at. Standard Starfleet issue – just like everything else in the room. Like everything else on Voyager, it was brand new – not even a scratch or a mark on it. It dropped to her side, still tightly clutched in her fingers, and her eyes closed as her headache started to pound again. She slowly sat down on the couch, putting the phaser up on the window ledge behind it and staring at it again. Having to wear it within her own ship was yet another reminder that life as she knew it was finished.

She had no idea how long she had been there before the unfamiliar stars started to blur in front of her. The tears came fast and hard, one arm hugging her torso as her head fell against the arm she had rested along the back of the couch. Her crying was guttural, the realization of losing her life now falling on her as a ton of emotional bricks. She had no concept of time, just the knowledge that her heart was being ripped in half and her body being turned inside out. The sobs eventually slowed, but she didn't move from her spot.

The sound of the door chime startled her, her headache giving her another sharp pound when she straightened up too fast. Quickly wiping the tears off her face and hoping that her makeup wouldn't give her away, she cleared her throat and drew a few deep breaths before calling, "Come in."

Chakotay was standing at the door, flanked by a pair of security guards. One of them looked to the captain, waiting for her nod of approval before moving back. The Maquis leader took a small step inside and looked around the room until he spotted her to his left. "I hope I'm not bothering you, Captain."

She shook her head. "Not at all. What can I do for you?"

He came the rest of the way inside, the doors sliding shut behind him with a soft hiss. Her rigid posture and tightly controlled voice told him immediately that she had been crying, but he let it go, instinctively knowing that the last thing she would want was to be found out. "I'd like to talk to you about what's going to happen now," he told her, fighting down the nervous tension that filled his stomach, "with my crew."

The captain gestured for him to sit down on the other end of the couch. "I've been thinking about that as well, Captain," she said. "I'm sorry about the Liberty. She was a fine ship."

"She was a broken down rust bucket that was barely able to travel at warp." He sat down opposite her, eyes glancing at the business end of the phaser that separated the two of them. "I never thought I would, but I'm going to miss her." Her prisoner allowed himself to smile for just a moment, but quickly tamped it down. "Well, you ultimately got what you came for," he said, getting straight to the heart of the matter. "Capture Chakotay and his Maquis renegades."

"I did," she agreed softly. "But it didn't exactly go according to plan." Janeway smiled when he chuckled, pleased that at least he seemed to have some sense of humour. She got up and went to the replicator to order some coffee. "Can I get you anything?"

"Just some water would be fine," he told her, very aware of the trust gesture she had just made by leaving the phaser on the window ledge beside him. "What will you do with us?" he finally asked, braving the question.

"Well, according to Starfleet's directive, I'm to immediately place you under arrest," she explained as she handed his glass to him, "and you spend the rest of the trip home in the brig." Her face was unreadable as she sat down again, taking the time to cross her legs and exude the air of authority that she usually managed to carry. "But Voyager's brig is only designed to hold about ten people, and the rest of your crew would be locked down in quarters until we get back to Earth."

Chakotay frowned a bit as he watched her, trying to guess where she was going. "Doesn't exactly sound comfortable."

"No, it doesn't." She took a swallow from her mug, then rested it back down on her thigh. "There is nothing in Starfleet regulations that fits this situation. And I'd be kidding myself if I thought that your people were even close to being happy about being stuck on board a Starfleet ship."

"That's putting it mildly," he said. "Most of them specifically left Starfleet to join the Maquis."

Deciding to see what he was made of, Janeway leaned forward a little and questioned, "And what about you? How do you feel about being stuck aboard my ship?"

It was a question that he hadn't expected; he had thought her to be more of the diplomatic type than a straight shooter, all evidence earlier in the day to the contrary. After taking a while to think about it, he decided to be honest. "I'm not very happy about it either."

"And I am not pleased with the prospect of supporting forty prisoners in addition to my regular compliment, with no guarantee of supplies and no support system. But I have no intention of putting you off the ship at the next convenient planet." Sitting back, the captain fixed him with a look as she contemplated him. "So what do you suggest?"

Surprised that she was even willing to hear his ideas, he faltered for just a second before he said, "Well…instead of having to take care of us, what if we could help you instead?"

She was equally surprised herself. "Go on."

Chakotay shifted in his seat a little, obviously pleased that she was going to let him suggest what he'd come here to say. "Starfleet trained or not, my crew is skilled. And I know you lost a number of people when Voyager was brought out here."

"You want to join my crew," she skeptically stated.

"Well, maybe merge is a better word." He thought for a moment. "Captain, I know that having us join your crew goes against everything you came after us for in the first place. But I, for one, am not ready to spend the rest of my life languishing in a prison cell. We can earn our keep."

The captain's expression was solid, her emotions kept carefully below the surface. "And what does your crew think of this idea?" she asked carefully.

He matched her look with a sternly set one of his own. "I'll make them like it."

A small smile crept into her features. "You haven't told them yet?"

Chakotay shook his head. "I told them I was going to speak to you. I didn't say anything about what my proposal was going to be."

Kathryn couldn't help herself and chuckled. "Well, I appreciate your candor, Captain." She set her mug down on the table in front of them. "The truth of the matter, Mister Chakotay, is that I was actually considering the same idea. In light of our circumstances, it doesn't seem practical to imprison any of you." Thinking for a minute, she considered what she needed to say carefully. "I would be willing to have your crew join mine, and integrate them into every department based on their skill set. With two conditions."

His grip tightened on his water glass. "Which are?"

Her gaze on him hardened just a little bit. There was no room for negotiation on either point. "First, this will remain a Starfleet ship and crew. I'll give your people some time to adjust, but eventually they will be expected to live up to Starfleet standards."

The Maquis leader grimaced slightly, knowing how hard a sell it was going to be. "And second?"

"I need a new first officer," she told him, seeing the surprise flicker through his eyes, though he didn't flinch. "I did consider Tuvok for the position, but in light of our situation, I need him at Tactical. You have command experience, and combined with your teaching background and your advanced tactical training, I think it makes you a good choice for balancing starship and battle operations with personnel issues."

Chakotay considered her offer carefully, mulling over his options. When it came right down to it, he didn't have any, and he knew it. "Agreed," he finally said, slowly nodding his approval.

"Good." She got up, and extended her hand to him once he was standing. "Welcome aboard, Commander."

He shook her hand, feeling somewhat comforted now that an agreement had been reached but still not happy with the overall picture. "I'll inform my crew of our decision, Captain."

"Report to me in my ready room when you're done. We can go through crew and housing assignments, and I'll get you up to speed on Voyager and her operating systems." He nodded and turned to leave, and she let him get a few steps toward the door before stopping him. "There is one other thing, Mister Chakotay."

Her first officer turned back to face her. "What's that, Captain?"

Now she slipped into full command mode, signaled by the practiced placing of her hands on her hips. "You and Mister Paris are going to have to figure out some way to co-exist on this ship. I am making him our new pilot, and I will not tolerate any sort of bad blood between the two of you," she told him, her voice dropping low before adding, "or between him and anybody else."

There was no mistaking her meaning, and he got the message loud and clear. "That won't be an issue," was his somber reply. "Much as I would love to slam him against a bulkhead right now, I'm afraid my life belongs to him."

The captain looked at him for a moment, again appreciating his honesty but at the same time uncomfortable with his open hostility toward her mentor's son, and confused as to what he meant. Deciding to leave it alone for the moment, she simply said, "Dismissed."

Though it took a little while, Chakotay eventually managed to find his way down to Cargo Bay Two after Janeway removed the guards that had been shadowing him. He now strode through the doors, steeled against what he knew was going to come. His crew were milling around, speaking to each other in hushed whispers and keeping wary eyes on the guards that stood just inside the doors to the corridor. They all converged on him the second the first one saw him.

"Chakotay, what's going on?" Seska snapped at him, clearly at the end of her patience.

"Just be quiet a minute and I'll tell you," he told her coldly. Her sarcastic temper was the last thing he needed to deal with now. When all eyes were on him, he announced, "Captain Janeway and I have reached an agreement. You all will be allowed to join Voyager's crew, and you will be assigned to positions that best suit your technical skills."

The howl of protest was loud and immediate. "You have got to be kidding!" B'Elanna snarled, her expression one of pure hatred. "How can you agree to this?"

"Quiet!" Chakotay shouted over them. It took a minute, but they eventually fell silent again. "I don't like this any more than you do," he told them, "but we don't have a lot of choice here."

"We could take their shuttles and go off on our own," Kurt Bandera suggested, getting a murmurs of approval.

"And what?" Mike Ayala questioned, surreptitiously stepping forward to put himself between Chakotay and the others. "Their shuttles top out at warp three. How is that any better?"

"Well we can't just sit here under that woman's control!" Seska snapped.

"That woman…" Chakotay shot at her, "is the only reason that we're not locked in the brig right now." He could see the idea already forming in his old lover's head, and so he added, "And if anybody here even thinks of taking over the ship, I'll throw you out the nearest airlock myself." He looked at each one of them, his heart constricting just a little when he saw the anger and disappointment in their eyes. "You'll be assigned quarters and duties as soon as Captain Janeway and I create the new duty roster."

"You…?" B'Elanna looked horrified. "What are you saying?"

Chakotay faced her with as much emotional shielding as he could. "I am Voyager's new first officer." Again there was a roar of discontent that he had to quell. "Hey, taking on that role means I don't spend the rest of my life locked in two metre by two metre cell, and that I actually have something to do so I don't go crazy!" He looked over to Ayala for some backup. "Mike?"

His friend thought it over long and hard, but to him the conclusion was inescapable. "I don't see that we have any choice," he said, pledging his silent support.

"Well I'll be damned if I follow you back into Starfleet," B'Elanna growled as she stormed out, followed closely by Seska and a pair of security guards.

Chakotay watched them leave, but didn't follow. "You don't have to take the offer," he told his remaining crew, "but I can tell you that you won't have any freedom, and you'll most likely be locked down in quarters. You might be able to live as civilians, but Captain Janeway has made it clear that anybody on this ship has to pull their own weight, or be imprisoned. Or your other option is to leave the ship if we find someplace that is willing to take you, and spend the rest of your life here in the Delta Quadrant."

Bandera grimaced. "Doesn't leave us much options, does it?"

Chakotay shook his head. "No." He looked to each of them once again. "It's ultimately your choice, but expect each of you to give Captain Janeway the same respect that you've given me, regardless of whether you join Voyager's crew or not."

Morning came all too quickly, and Chakotay was slow in getting on the move before his first shift as Voyager's first officer. He sat at the edge of his bed as he sipped tea, something that he hadn't really done since the last time he had ever had to report for duty on a starship. The uniform that was neatly folded on the lounging chair next to the door to the living area seemed to stare back at him, taunting him. Its design was different than what he previously wore, but it still held the same connotations, the same regimentation and the same harsh memories that it had when he'd left years before.

His agreement with Captain Janeway left the decision of donning the Starfleet uniform up to each individual Maquis, but he had decided right away that he would, as his own show of good faith to her, and to set an example for his crew. He hoped that eventually they would come around to the idea of integrating themselves into one crew. He thought back to B'Elanna's reaction when he told them about the deal, and he wondered whether or not she would actually ever come around at all. The idea of seeing her talent go to waste bothered him.

But there was no more time to think about it right now. He got up and set the cup down on the dresser, thankful that it had been empty when he'd been given Commander Cavit's former quarters. His reflection looked back at him from the mirror, showing a man who was very much at a crossroads in his life. Chakotay looked back at himself, seeing someone who, despite middle age, was still in relatively good shape, and who seemed to be carrying the weight of the universe on his shoulders. It suddenly occurred to him that what had happened, while a tragedy for most of the people on board, was a gift to him. A fresh start. One that might just challenge him in ways that he hadn't been before. Here there was no opportunity to run, or to flee in anger when his ideals didn't match those of his new elder. He would have to learn patience, and how to fight for what he believed in all over again.

The uniform fit perfectly, as he'd expected it to after the computer had analyzed his clothing needs. It still smelled new, a bit of a chemical scent on the fabric from the replicator, and it was a bit stiff, but surprisingly comfortable. He felt just a little bit of hope fill him, and as he strode out into the corridor toward the turbolift, he started to feel optimistic about how the first day of his new life would unfold.