Explanation: The comment, "She's like my daughter," by the Doctor relates to some history that Phoenix and the Doctor have and I don't go into this much as it is looked at more in another story I haven't posted yet and won't yet. The section in the third paragraph about Torchwood relates to this other story too, when Phoenix and Jack first met.
The section between these **** is a flash back from Jack.
What Do We Do.
Phoenix sits on the bench she sat on a couple of days ago, alone in the dark, no-one around her. She looked out at the moon reflecting on the sea, the light sparkling on the surface of the mass expanse of water ahead of her. If there wasn't proof before that she was alone before, there was now. She was alone in the bay, alone on Earth, alone in the universe. She knew how the Doctor felt, both of them being the last of their kind but not starting out that way.
There was one major difference between them. The Doctor had known his race, had a family, had children, been apart of their lives before it was cruelly taken away from him. At least he had known them all, had the pleasure and honour of being with them before they were taken away. He had the memories of family, of love. She had never known her family. They had all died long before she was born, century's before she was created, not born, created. She would never know them. They had been lost and sealed in time, she had tried to find them, tried to go home but she couldn't. Even the Doctor couldn't help her.
She had known love but all too briefly. She had known love from parents, her adoptive parents here on Earth. They had loved her since she was 10 years old. Mr and Mrs Adams. But as it was in her life, that love would never last as they were killed in a car crash on her 18th Birthday. Her next love was Jack. Captain Jack Harkness of Torchwood 3. Cardiff. She had met Jack after a Weevil attack and after the Retcon failed, she looked for him. She ended up becoming a part of the Torchwood team but that was still to happen. She loved Jack and Jack loved her but that wasn't meant to be either and she left Torchwood after less than a year, after and huge battle.
That was when she became the Dark Avenger. Travelling through time on her own, defending the weak and the defenceless. Using her abilities to help other people that couldn't help themselves. Never getting close to anyone until the Doctor. They ran into each other on a planet and after Phoenix had finished her own little mission, she travelled with him in the TARDIS. Then came the day he left her. They had been on a planet with it's inhabitants hell bent on destruction. Adina took action and the Doctor left her, left her behind as he didn't agree with her actions. Left her in the universe alone, no idea of where she was, clawing her way back to civilisation to be alone again.
She never really left Earth after that. Her heart was always on Earth, even when her body wasn't her heart was. Her heart was always with Jack though he didn't remember, she had made sure of that. Every now and again she would return to Earth, return to Cardiff. She would watch the team from the shadows, be there when they were working, never in the hub, only in the open where she could hide. Once or twice Jack had seen her but he never knew who she was, the mind wipe she had done on him was more effective than Retcon as she took the memories away so there was nothing to trigger.
She watched as Jack fell in love with little Welsh Ianto Jones, breaking her heart as they became closer and closer, wishing she could stand in front of him and give him his memories back, memories of them and their love. Then there was their future, Jack's past and her future. Their new love remembering their old love, her remembering their old love. Their son, the battle and then, alone. Alone again, walking and fighting through time. No-one by her side, no-one to come home to, no home to come back to.
Now she was alone again, back on Earth, back in Cardiff, back with Jack. He was close enough to touch, close enough to hold, close enough to kiss but yet so far from her touch. She had touched him, held him, loved him, back on the dead planet, that one time but now she held both memories of that, his memories and her own. She had wiped their intimate time together from his mind and took it into her own, two memories, two sets of feelings. As she sat on the bench, her knees to her chest, her arms wrapped around her legs, her eyes filled with tears focusing on the sea, the dark, calm sea, thoughts running around her head.
"Why am I doing this? What am I fighting for? What am I sacrificing myself for?" she asks out and there is no reply, sat alone in the dark of the bay.
As the Doctor works away in the TARDIS, still sat in the middle of the hub, Jack sat in his office, sat almost in complete darkness, the only light in the office were stray beams of light coming from a lamp in his bedroom. He looks at the open hatch in his office knowing that Ianto Jones, the beautiful Welshman he had fallen in love with, was asleep in his bed, asleep in Jack's bed but he also knew that Phoenix was alone on the dark streets of Cardiff, afraid, hurting and in pain. He was torn and he knew it all to painfully.
His love for Ianto Jones was a new love but a strong love. He hadn't seen Ianto that way from the started. It sounded strange to say it but Ianto had grown on Jack. Whenever Jack was down, Ianto was there to pick him up. If Jack needed a helping hand, Ianto was there. If Jack needed to let go of anger, cut loose, Ianto was there and forgave him every time. Over time, Jack had seen his feeling change for Ianto, growing into love for him. Jack couldn't imagine life without Ianto though he knew at some point Ianto would die and leave him, that was his curse, to out live everyone he loved, everyone but Phoenix.
His love for Phoenix had almost been instant, almost love at first sight. The moment she walked into the office of the Time Agency and removed her helmet, Jack fell for her. At first, he kept his feelings under control but when he saw that she felt the same about him, that they had both fallen for each other, he let go. They tried to keep it professional, they were partners in the Time Agency, completing missions together, having each others backs but soon it was more.
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One particular mission didn't go the way it was planned and quickly went bad. It ended up with a battle with Phoenix and Jack against a small army of between 50 and 100 troops. It got to the point where they were almost back to back in the middle of the troops, the army surrounding them. From nowhere, Phoenix turned to him and drove her sword right through Jack's heart.
"I'm sorry Jack but I have to," Phoenix tells him, trusting the rest of her sword through his heart and out of his chest, his eyes lost their life and as he died, Phoenix pulled her sword out of him.
He came back to find himself laying on the floor, blood down his shirt with a slash in it from where Phoenix had stabbed him. He turned to find Phoenix sat on the floor next to him, one arm wrapped around her ribs, the other resting on top of her knees which were bent up in front of her. She spits out another mouthful of blood and looks at him. Blood running down her face on both sides from various gashes. Her pants torn, her top torn. Jack couldn't see blood as she was wearing black but he knew it was there.
"Sorry Jack. I had to do it," Phoenix tells him and then she coughs and spits out another mouthful of blood.
"You had your reasons. Are you ok?" Jack asks her getting to his feet and offering his hand to her.
"Nothing that some down time won't cure," Phoenix tells him taking his hand and he helps her to her feet though it was painful for her.
Jack puts his arm around her and is about to slide his arm under her legs when she side steps.
"What do you think your doing? I can walk you know," she tells him and he gives her a look that only he could give.
"Stop being so stubborn. You can barely stand let alone walk," he tells her and with that, he picks her up into his arms and carries her.
They arrived back at the hotel and Jack lays her down, helps get her clothes off and then he stands back and sees all the wounds she had sustained and there were a lot of them. Jack cleans her wounds but doesn't dress them at her instants that they will heal soon. Once the wounds were cleaned, Jack took his coat and boots off and lay on the bed next to her, stroking her hair and shoulder as she closed her eyes, allowing her body to heal as she rested.
"Why did you kill me, though temporarily?" Jack asks her, almost whispering in her ear as he moved a little closer to her, tracing the out line of her tattoo with his finger.
She explained to him about Adina and the fact that if he had been alive, she would have drained all the life out of him, killing him for real as that is what she had done to the army in the end. She explained that she was protecting him and she always would. That night was the first time, while she was still healing, that they made love and it was the first of many times.
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After he left her, left her to die and then came back to find her gone, he mourned her. He mourned for weeks for his lost soul mate. He finally found someone he could share his life with, share time with and wouldn't grow old on him. He lost the love of his life because he was too scared, he was scared of Adina, scared to actually watch her die. He had been a coward and he had lost the woman he loved because of it. Then she was back, back in the hub, back in his life and he loved her all over again. And then he found out that she was pregnant with his son when he left her there alone.
He wanted a child, he had done for a while and while he had been with Phoenix, he had thought about having a child with her, he loved her that much. Then to find out century's later that she was pregnant with his son and that if he had of stayed and fought with her, she might not have nearly died, his son could have survived and they would have been a family. He would have been a father to the child he craved with the woman he loved.
He looked over to the hatch again and he was torn. He was torn between the man he loved Ianto and the woman he loved Phoenix. He couldn't take it anymore and he got up from his desk and walked into the hub. The door of the TARDIS was open so Jack went inside. It hadn't changed. It looked the same as last time he was in there. He looked around but he could see the Doctor.
"Doctor! Doctor!" Jack shouts out and it echo's around the TARDIS.
"Down here Jack," comes the Doctor's voice and he was under the centre console.
"What do I do Doctor? What do we do?" Jack asks him just seeing his legs.
"That's not something I can answer Jack. You know how she feels about you and you know how you feel about her. It's down to you two now," the Doctor tells Jack finally appearing from under the console.
"Will she survive this Doctor and be honest with me?" Jack asks him knowing that the Doctor would be honest with him without having to ask him to be.
"She is tired and weak Jack. She has lost that spark, you've noticed it. She is worn out. She hasn't got the energy or the will to beat The Devourer so she will consume it and it will burn her out. Where she is at the moment, she won't survive this Jack so I would start thinking about saying goodbye. I will be," the Doctor tells Jack and at that precise moment, his mind freezes and his heart breaks.
He was going to lose her again but this time for good.
"What do I do Doctor? Help me," Jack almost pleads, tears now falling down his face.
"I can't help you like that Jack. I don't know what to do to help Phoenix either and I know a hell of a lot. She's like my daughter and I can't help her," the Doctor tells him, feeling his pain.