Disclaimer: I do not own anything to do with Star Trek Voyager.

A/N: Well, this is my first Voyager story, so please don't eat me! Not a lot to say really, except that reviews do mean a lot to me, especially as this is the first one involving Voyager that I have written (I primarily write Naruto and Final Fantasy 7 stories, so feel free to check those out too!). Reviews are very much appreciated, as if I don't get any for a while, I kind of assume that people don't like the story, and stop lol. I am not going to say 'won't update until I get 5 reviews' as that's silly, in my opinion, but I do like to know how I am doing.

Anyway, enough of my rambling! This will be a multi-chaptered story, so there will be more to come!

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Nobody Ever Sees These Things Coming

It felt good to be in the Alpha Quadrant again, but at the same time, it filled the captain of Voyager with a sense of dread. Not everything felt right, things felt different…both on her ship, and in Starfleet. She had heard the rumours from some of her closest friends in Starfleet, but she had not listened. Rumours, that was all they had been, but now that she was back in Federation space, she was beginning to see what some of her dear colleagues had meant.

Kathryn felt like she didn't know some of her crew anymore. Seven had been feeding her every excuse under the sun, as the former Borg did not want to go to Earth for fear of what people would think of her, no matter how many times the captain tried to assure her friend that she would not be judged. However, deep down, she knew that there would be some people who would have a problem with Seven, and the captain felt helpless, but she couldn't do anything about the thoughts of others.

Another problem that the captain had was that the friction between the Maquis crew and the Starfleet crew was making itself known again. The Maquis were worried about what greeting they would receive when they returned to Earth, and a few Starfleet officers wanted them to be placed under arrest when they got back to Starfleet Headquarters.

The closer they got to Starfleet, the larger Kathryn's headache became.

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B'Elanna was nervous to be returning to Starfleet, and not just because she had been so accustomed to living in the Delta Quadrant, but because she was unsure about the futures of her, Chakotay, and the other Maquis members. She had experienced her fair share of fights with members of the official Starfleet crew during the past few months, and she had a feeling that it would be the Maquis against Starfleet when they returned home.

With a sigh, she tapped her commbadge.

"Torres to Chakotay. Could you come to my quarters please?" she asked.

"OK, on my way." Was the response, and the communication link ended. B'Elanna sighed again and walked over to her replicator, getting a coffee for herself. She needed something to try and steady her nerves.

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Kathryn had retired to her ready room, leaving Tuvok in charge. She knew that Chakotay was trying to keep the Maquis members in check, a few of them had started to cause trouble, so she excused him from bridge duty. Now they were back in familiar territory, she felt they didn't need to be as defensive and alert as they had to be in the Delta Quadrant. Just as she was reading one of Tuvok's security reports, her console alerted her to an incoming transmission. It was from Starfleet.

"What can I do for you, Admiral?" she greeted. Her superior just sighed, obviously not in the mood for formalities.

"I understand that you have Maquis members on your ship." He said, and suddenly Kathryn felt like she wasn't going to like where this conversation was going to go. Maybe Chakotay and the other Maquis members were right to be concerned.

"Yes, they have been loyal members of my crew these past few years. Commander Chakotay and the rest of his crew have been of a great help, and are as much a part of my crew as the official Starfleet officers. Why do you bring this up?" she asked, and the Admiral looked down for a moment. By building them up, Kathryn hoped that he would say that the Maquis would be treated as normal, and not as criminals, when they arrived at Starfleet Headquarters.

"They are going to be placed under arrest and tried at Headquarters. I'm sorry, Captain, but they are still criminals, no matter how much they have helped you and your crew. I suggest you inform them. I have other work to attend to, welcome back to the Alpha Quadrant." The Admiral said and ended the transmission.

Kathryn let out a frustrated sigh, she knew the Admiral was a busy man, but she couldn't help but think that he had gone so quickly so that she could not argue. It frustrated her, but there seemed to be little she could do. She only hoped that Chakotay would take the news well. Part of her wanted to tell him now, but the problem with that was, she didn't know how to.

Not only that, but she didn't want to put their relationship in jeopardy.

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Chakotay was finally at B'Elanna's quarters. He had a rough idea of what she wanted to talk to him about, but he did not know about her worries or concerns. It took her seconds to tell him to enter, and what the first officer saw shocked him. His friend had never looked so subdued, or so quiet.

She must be really worried. Chakotay thought as he took a seat opposite the half Klingon woman.

"What's going to happen to us, Chakotay?" B'Elanna asked, looking at her tattooed friend with worried eyes. Chakotay sighed, not sure what to tell her. He was just as worried about the Maquis crew members as she was, and he intended to speak with the captain, though he wanted to speak to her anyway about other matters.

"I don't know, but I wish I did. Starfleet may caution us, they may let us go. I have no idea, but I intend to speak to the captain, as she may have heard something from Starfleet Headquarters. As soon as I know something, you will be the first person I come to, so we can tell the rest of the Maquis members on this ship together." He said, and was pleased to see a smile find it's way onto his colleague's face.

"Thank you, Chakotay. That means a lot to me, that you trust me to come to me first." She said, and Chakotay let out a laugh.

"You have been my friend for many years, B'Elanna, of course I can trust you."

Before anything else could be said, Janeway's voice filled the room.

"Janeway to Chakotay, come to my ready room immediately."

"On my way. Perfect timing, I'll make your concerns known, B'Elanna." Chakotay said with a friendly smile. Torres nodded and watched as her comrade left her quarters.

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I have no idea how I am going to break this news. I don't want to lose you, but I fear I will. I don't want to lose anyone, you and your own crew have been wonderful assets to the overall crew of Voyager. I remember when we finally admitted we had feelings for each other, why does it feel like our time together is being cut short?

Janeway's inner thoughts were cut off when the door chime sounded and Chakotay walked into the room. The captain gave him a sad smile, then walked over and embraced her lover.

"I'm so sorry."

Those three words filled the man with dread, this wasn't going to be a pleasant chat, he could feel it.

"I take it the Maquis members aren't going to be welcomed with open arms?" he asked when Kathryn let him go.

"They want to arrest every Maquis crewman on this ship, that includes you, B'Elanna, and I imagine Tom as well. The Admiral cut me off before I could argue against it. I told him how I have come to trust and befriend nearly every member of the Maquis on this ship over the years, but he would not listen."

Chakotay sighed and watched as Kathryn turned to look out of the window. This was certainly a mess, and he wasn't sure that Voyager's captain could sort this one out. The first officer was about to respond when Kathryn's console bleeped, telling her a transmission was coming through. There was a fleet ready to greet them, the ships were visible out of the windows now, and the captain's heart filled with dread. Pressing a button on her console, she saw the face of one of the security officers at Headquarters. He looked unfamiliar to her, though she was sure there had been many staff changes at Starfleet while Voyager had been gone.

"Captain Janeway, welcome home. Is it a good time to beam a security team aboard to deal with the Maquis members on your vessel?" he said, obviously not caring for pleasantries. Kathryn sighed and looked at Chakotay briefly. She had never felt so awkward or upset in her life, but she was stuck between a rock and a hard place. Looking back at her screen, she sighed.

"Yes, my chief of security will meet you in Transporter Room One." She said, and ended the transmission.

"So that's it then…well, thank you Captain, but I have to go and speak to the Maquis crewmen." Chakotay said, and began to head towards the doors.

"Chakotay, wait!" Kathryn said and ran to grab her lover's arm, though she was not sure if she could class him as her boyfriend anymore.

"Save it, Kathryn. I have a crew to speak with." He said coldly and shook his arm from her grip before leaving the room.

Janeway had to fight to keep the tears from spilling.

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A/N: Well, my first Voyager fanfic…hope I am doing ok. One of the worst things about starting a new fic is wondering if anyone else has done the idea already lol. Anyway, thanks for reading and please review! Flames will be used to roast marshmallows, but I am open to constructive criticism, as this is my first Voyager fic.