As a leader of the Maquis and a Commander onboard Voyager, loyal to Captain Janeway and very devoted to the crew which he called a family. Himself as Commander Chakotay of the Maquis had finally found a place where he and his Maquis crew could fit in and they really became one with the crew. As the years went on by, the bonds between him and his Captain as well as the crew and ship became tighter, a few bonds broken, a few new ones created. Chakotay and Kathryn had a special bond that the whole crew could see but the Command Crew never saw it over their 'Prime Directive'. But there was a time when they finally noticed how great their bonds were, it all happened when they unintentionally took in a virus which caused them to live on a planet with something in the air that kept them alive. Chakotay had suggested to Kathryn many times to stop the research for a cure and to live out their lives on the planet but Kathryn refused, until one day, there was a storm. Kathryn's research was damaged beyond repair, there was nothing to salvage from it. As the days wore on, Kathryn and Chakotay became closer until Voyager came back for them with a cure, when they arrived back onto Voyager, they weren't as close. They were just the Command Crew as they left behind their feelings on that planet with the lonely monkey. Later on, Chakotay finally convinced Kathryn that it was time to 'look back' so that they could move on without any more troubles.
The two became better than just best friends, they were finally a couple and the crew was more than happy for them. Eventually one day, it was Christmas and the crew were out celebrating in the Mess Hall when Chakotay went with Kathryn, he had announced to the crew for their attention, he turned to Kathryn and got onto his knee and asked her to marry him, with that she said yes and everyone else was excited for them. But the day had turned to disaster. Voyager had gotten under attack a few moments after, they called a red alert and headed to the Bridge, Voyager had won but the ally ship that had joined them on the battle needed their help. Chakotay volunteered to go over and help the other ship. Kathryn said no at first because she wanted to go but Chakotay insisted that she stay and have him go, she eventually gave in and allowed him to go.
Chakotay had gotten into the Delta Flyer by himself and he left the shuttle bay and headed towards the ship, not knowing they were the real enemy. He entered the other ship and helped them with their repairs before heading back to Voyager but that was when everything became even worse. The alarms inside the Delta Flyer went off and it indicated that the ship had raised its shields and engaged their weapons, he tried to hurry back to Voyager when he realized there was no time. "Kathryn, there's no time, go to red alert now, they aren't who we thought they were. I'll be in as soon as I can." He turned his ship around and fired at the ship as soon as it began firing at Voyager, he tried to fight them off as much as he could but they were too strong now that they were repaired. He could see that Voyager wasn't ready, the repairs weren't done, their shields were down and as were their impulse, they were sitting ducks. "Kathryn, I'm sorry, I love you." With that he drove towards the ship on an collision course, with shields raised to the maximum and he stood to the back of the ship, watching as the ship neared and collided with the other.
Onboard Voyager, the entire crew was watching as the ship collided and the other destroyed, Kathryn heard his voice and she knew what he was going to do and she tried to tell him not to do it, she tried to tell him she loved him but nothing would work, all she could do was stand and watch it happen, her mouth wouldn't move, her knees were buckling, but a moment later, she spoke to the crew and announced what happened and gave a speech as her voice cracked. She returned to duty, still in shock as to what happened. The entire crew didn't know what to do, even the former Maquis had thought of leaving Voyager because their leader had gone.
Minutes felt like hours, hours felt like days, days turned into weeks, weeks turned into months. Kathryn was still in shock over what happened, until another Chakotay came from the Q Continuum. Kathryn had fallen in love all over again, a few weeks later, she had forgotten about the loss of her fiancé. Everything was the same for her again, but not to the crew. This Chakotay was different for them, but it was the same for Kathryn.
An year later, the Chakotay that the crew had thought to be dead was still alive and barely surviving on a planet that his new friends beamed him to before the ship collided. Chakotay was never happy there. He made his own ship, but it took hard work and days without sleep or food. He was very eager to get back to Voyager, which he called his home. He had said his final goodbyes to his friends before leaving the planet, he couldn't wait to take a shower, eat til he was full and get his sleep. He missed everything but there was one thing he missed the most out of everything, Kathryn. He decided to take naps now and then but it was only an hour each as he hurried to get back.
Another year had gone past when he finally found Voyager and he was now happy as he clicked on his communication and he spoke. "This is Chakotay." He told them their code. He was so tired that he didn't hear the last word he spoke out before passing out, which was 'help.'
A week later, he woke up in the sick bay of Voyager, his whole body felt stiff and tired as he sat up and rubbed his head as it began to throb. He stood up a bit too fast and felt a hand on his shoulder, making him sit again and he sighed. "Thanks." He didn't think to look up to see who it was as he rubbed his eyes and blinked as he finally looked up and he saw Kathryn. "Kat-" He coughed and looked up again as she told him not to speak and to listen and he just nodded as he listened to her as she filled him on what he had missed over the last two years, he was devastated at the loss of some members and the chance of missing out on seeing his two kids birth.
Another week later, he was released to his quarters but he was confined there so he could rest and heal some wounds that would be scarred forever against him.
Chakotay felt like he didn't want to be there, he felt like hiding. He hated that feeling when he felt like he didn't deserve anything at all. He was asleep when Kathryn had snuck into his quarters and she sat there as she looked at him, knowing the other Chakotay was on the bridge, but she didn't know that behind the man was Q.
Chakotay woke up to see Kathryn looking at him and he sat up on his bed. "Kathryn." He looked at her again and looked at her hand and saw another ring to the one she had from him. "Oh." He sighed softly and got up to go to the shower as Kathryn spoke and he just nodded, feeling more left out more than ever. Until the day Kathryn had found out that the man she was married to was Q, how did she find that out? Well, Q had lost his powers from using his so long as he pretended to be Chakotay in her eyes. The crew tried to tell her but she wouldn't believe it. She divorced Q secretly and she tried to get Chakotay back but he was there in reality but his mind wasn't. She felt so bad so she decided to leave him alone until he was ready.
As another year went by, Chakotay wasn't talking to Kathryn still, his mind wasn't there but he was there, he was just on auto-pilot. Kathryn was tired of being alone so she went to talk to him, the doctor was there to help him and they eventually pulled his mind back into reality, he had started to act more like himself, eventually Kathryn gave him his old Commanding job back and he became himself and Kathryn fell in love with him but she knew she had to give him time.
A few weeks later, Chakotay had asked her for dinner and it progressed greatly from there. Several months later, they became a couple and fell in love once again, in Kathryn's eyes, Chakotay treated his kids as if they were his own, and he was a wonderful father. They came under several attacks but they always came out with several damages but they were always repaired. A while later Chakotay finally proposed to Kathryn again and she said yes, this time she believed it was really him, Chakotay was happy once again. He felt like a family again, he couldn't believe how far he had progressed from the beginning with everything, the crew was happy to have him back.
One day there was another surprise, one that Chakotay didn't tell anyone about, he wore his formal Starfleet uniform as he told the crew to dress formally as he met everyone else in the mess hall and he remembered Kathryn walking upon the 'aisle' she didn't know about until she got to Chakotay and asked what was going on. "We're getting married Kathryn.." He grinned at her as the Doctor had began the ceremony and at the end he kissed her and they were officially married. Kathryn smirked as she had a surprise for them too. "Well, that's a surprise but I have one too.." She looked at the crew. "We should be expecting another addition to the crew in nine months." She smiled as the crew were confused until they figured it out and cheered for the now married couple.
A year later, they had a new addition to the crew. Everyone treated the baby as if they were their sibling, a few weeks later, someone suggested a childcare on Voyager and they thought it was a great idea so they decided to make a new room onboard and they had a childcare a week later. But everything became worse again.
Chakotay had to go to the planet and help some other people and they had a deadline for when he had to return to Voyager and he missed it because he got lost on the planet, but he found a way out eventually and returned to Voyager. Everything was fine, Chakotay began to have a relapse on his feelings for when he had gotten stranded on the planet and when it took him two years to get back to Voyager, his mind had gotten lost in space once again. Kathryn felt like she couldn't handle it so she divorced him and Chakotay's state had gotten worse with each day that had passed, soon enough he had gotten confined to sickbay and quarters.
Kathryn found another Chakotay that wasn't Q this time, it was a Chakotay from another reality, she fell in love with him and Chakotay reached that point where he could no longer handle it or hang on. He snuck out of sickbay when the Doctor was deactivated and he left his communications device in sickbay as he went to the shuttle bay. "I can't do this.." He hesitated on deciding whether or not to run out of the shuttle bay into space, he stood there as he looked out, he felt so bad again because Kathryn had gone and married another man because he wasn't himself, he hated causing pain and burden for Kathryn, so he got in the shuttle as Voyager was stopped because they needed more repairs, he got into the Delta Flyer, just when everyone noticed that Chakotay was gone, he lifted the shuttle off and planned on going for a small trip around Voyager, not knowing that Voyager had automated systems, since their last update, Chakotay was never told about that, so he flew around and Voyager detected it as an enemy and Kathryn tried to stop the system in time, but it was too late. The system had fired and the shuttle had blown up already. He was gone, forever this time.