With the Doctor over the worst of the withdrawal symptoms, Jack decided to return once more to Torchwood. It was clear the Doctor wasn't ready to leave the house as he was still weak and prone to random mood changes that no one could predict. He also still hadn't dealt with what drove him to seek the drugs in the first place. Not that it mattered as Jack had refused to touch him anymore then he had to and while they still shared a bed as well as a home they were currently living two separate lives that were drifting farther apart by the day. At Torchwood the Doctor spent most of his time in Jack's room or hiding down in the morgue or another empty room just seeking time to himself. At home, he did the same by choosing to stay up in their room with only Emily for company until he was forced to descend the stairs in order to eat or get tea. It was clear they were both hurting but all the members of Torchwood heard were the angry hisses they shared at each other when they were forced to be in the same room.
It was clear over the next two weeks that Jack no longer trusted the Doctor's opinion on anything. The Doctor didn't even know why he was made to join in the meetings because whenever he spoke up his opinion was immediately rejected or Jack asked one of the other members of Torchwood to verify his findings. The Doctor eventually stopped talking during the meetings his eyes growing distant as he tuned them out. Martha tried to talk to him but he ignored her as well as he hid from the universe. Martha hoped that Jack would eventually pull his head out of his ass and realize how much the Time Lord was hurting but Jack seemed content in his anger of the man and not willing to let it go anytime soon. So she kept her distance until one afternoon she couldn't hold her tongue anymore. The Doctor had gone up to Jack's office only a few minutes prior with a cup of tea and coffee in hand in an apparent attempt to make amends but Jack ignored it. His angry words could be heard at Martha's computer as the door to his office had remained open a crack due to the Doctor's full hands.
"Damn it, Doctor, can't you ever clean up after yourself?" Jack yelled at him. The answer was the sound of glass breaking against the wall. She wasn't sure who threw the cup but she did know that she had been quiet long enough. Standing up, she stormed up the stairs to the office pushing the door open all the way. Inside, she found the Doctor sitting staring at Jack with his arms crossed as Jack glared back at him. Behind Jack, tea ran down the wall and broken glass littered the floor.
"That's enough," Martha snapped at the two men.
"This is none of your business, Martha. Now return to your desk before I suspend you for the rest of the week," Jack told her calmly his eyes never leaving the Doctor.
"No. I don't care if you do suspend me but I am not allowing this to continue. If it was just the two of you, I wouldn't interfere but you have a little girl who is caught in the middle of your childish behavior and I don't want to see her hurt by you two. So I am going to pick her up from daycare tonight and bring her home with me while you two either fix this or end it. I don't care which option you choose but neither one of you is leaving this room until Emily gets the parents that she deserves. Whether that means you raise her separately or together is your choice but this has to end," Martha scolded them. She turned slamming the door to the office as she stormed out of the room.
Both Jack and the Doctor didn't talk right away as they continued to stare at each other. The Doctor desperately wanted to seek the comfort of the drugs that he used, while Jack wanted a strong drink and to get laid. Neither one was an option as Martha was right they needed to talk. They were hurting Emily with their fighting and Jack had noticed the once happy little girl was becoming more withdrawn again at home. It was the same way she would act after the Doctor stayed away for more than a few days or disappeared suddenly but he couldn't blame the Doctor for her pain this time as it was both their faults she was hurting. Jack sighed as he ran his hands down his face.
"Martha's right. We can't go on like this anymore," Jack commented.
"I know," The Doctor sighed he glanced towards the TARDIS.
"I'm not unlocking her yet regardless of the decision we make today. We have another week before your month is up and I can tell you are still having cravings. Even if I am angry at you, I don't want this drug habit to kill you and if necessary, I will find you a new place to live until you are able to travel the universe again on your own," Jack informed him.
"I don't want to live somewhere else," the Doctor admitted.
"Then we do need to talk about what happened because there are a few things that I don't understand. Like how you can trust me enough to raise your daughter for you but not enough to tell me your actual plans for the Master or how you were planning on bringing him down. Instead, you tell me a story about an island of people that disappear then hand me over to him," Jack spat at him.
"The island is a real place that he was hiding. I don't understand why people disappear from there but I would like to investigate it further one day. And the reason I didn't tell you my real plan is because the Master had to believe that I was really turning you over in order for me to save Donna and everyone else that he was watching. If he thought even for a second that I was betraying him he would have given the order to kill them without hesitation. I knew that there was a good chance that I would lose you over my decision but I swear to you that I thought about it for as long as possible before deciding to take you there. I went through every scenario I could possibly think of and all of them ended with her death. I am sorry I hurt you in order to save them but given the choice to do it over I would make the same decision," the Doctor told Jack.
"So would I," Jack sighed. As much as he hated the decision he knew the Doctor had been right to make it. He could eventually give the Doctor for betraying and move past the anger he felt but he couldn't bring Donna or anyone else who was killed back to life. "I understand why you made the decision but it is going to take me time to forgive you for putting me in his hands again. Even if it was only for a few minutes, I kept thinking about the Valant and the year of torture we suffered there at his hands."
"You've been having nightmares again," the Doctor answered.
"I always have nightmares."
"Me too," the Doctor replied. Jack smiled softly at him.
"Is that why you started taking the drugs again?" Jack wondered. The Doctor looked away. This was the conversation he didn't want to have. He ran his fingernails slowly along his arm as he thought about his answer until he heard Jack clear his throat. Realizing what he was doing, he let his hand drop again. "We can get your body clean, Doc, but there is a strong possibility that you will quickly relapse unless we address the reason why you started using it again. So why don't you tell me the reason you felt the need to turn to drugs then come to me or Martha or anyone else who could have helped you."
The Doctor closed his eyes refusing to look at Jack as he bit his lip to keep from speaking the words that he had kept himself from acknowledging all these years. How could he tell the man that he lived with and was helping to raise his child that he was the reason he sought out the comfort of the drugs? Despite what Jack currently thought about him he did still care for Jack in his own way and feared that telling him would drive a wedge between them forever. It would be simple to open his mouth and lie to Jack instead but a lie wouldn't change what happened or stop Jack from taking his anger out on his body again. He took a deep breath as he realized that Jack was still staring at waiting quietly for the Doctor to respond. He let the breath out slowly as he opened his eyes. He refused to look at the Captain's eyes as he stared down at his own hands.
"There were several times I thought about taking them again but when I finally decided to take them again was after the night," the Doctor trailed off not wanting to say the words but Jack finished them for him.
"That I raped you," Jack finished. The Doctor's head shot up meeting Jack's
"I never said no," the Doctor argued.
"It doesn't matter that you never said no. You never gave me permission to hurt you either. You fought me that night and I held you down and forced myself on you then refused to look at or comfort you after. I was angry at you but I had no right to use your body that way or to continue using your body for my own pleasure after. I kept telling myself it was all right because you returned and laid with me but you deserve more than someone who uses your body," Jack told him.
"It has never mattered what I want in bed," the Doctor whispered. Jack ran his hand through his hair before turning in his chair. Opening the cabinet he pulled out two glasses as well as a bottle of whiskey. He poured them both a glass and the Doctor took it gratefully. He drank half of it down quickly before setting it on the desk. Jack drained his own glass then refilled it and topped off the Doctor's glass.
"But it should. You should have told me to stop or that you wanted to look me in the eyes while we had sex long before you actually allowed yourself to show me what you wanted. That night should have never happened and you should have hated me for it. I would have understood if you had taken Emily and never returned but you kept coming back and I don't understand why," Jack explained to him.
"I don't want to lose my daughter or you. I just wanted a family," The Doctor admitted. He fiddled with the glass giving his hands something to do in order to keep from scratching his arms.
"But you stayed away. Sometimes for weeks at a time," Jack reminded him.
"I am not good with relationships Jack. My first relationship was with Koschei. While Time Lords had no problem with same-sex relationships, my own family frowned upon it. I was forced into an arranged marriage that ended as soon as my youngest joined the academy. It was then that I ran back to him and stayed with him until I finally couldn't take it anymore and hide with the nameless of Gallifrey before leaving the planet for good. By the time I left him, though, he was no longer calling himself Koschei but had become known as the Master," The Doctor admitted trying to make Jack understand.
"Jesus." Jack downed the second cup of whiskey then poured himself a third. He had always suspected there was more to their friendship than the Doctor would admit but knowing that he had loved that monster made Jack feel sick.
"After that night, I wanted to stay away forever but I made the decision to return. Even if you never hurt me again, you were still angry so I only stayed long enough to make sure Emily was alright before leaving again," the Doctor explained.
"Because you were afraid I would hurt you again," Jack concluded and the Doctor nodded. "Listen to me, Doctor. What happened that night wasn't your fault. I was upset because Emily had called me daddy a few days prior and at the time I was still just her Uncle Jack. That still gave me no reason or excuse to take my anger out on your body rather than talking to you about it. Instead, I let myself become angrier and angrier until I lashed out in the worst way possible. I promised myself I would never let it happen again if you returned and I refuse to break that promise no matter how angry I get sometimes."
They both went quiet as they worked their way through another glass of whiskey each. It was clear to Jack that Martha was right and something needed to change but he wasn't sure that they could fix the relationship they had. There were too many trust issues that couldn't just resolve themselves overnight and the only reason they had even tried so hard to hold on to the other was for Emily. She was getting to the age now, though, that she would see the coldness they felt towards each other and it would affect her growing up. Jack didn't want her to end up in an abusive relationship when she was older because of what she learned growing up. The best thing all around would be to just end it but he didn't want that either. Even with all the pain a part of him still loved the Time Lord and that part had hope that they could work it out eventually. They just had to learn to communicate properly, something neither one of them were good at. Sure they could talk all day long about encounters they had while traveling and Torchwood business as well as nonsense but rarely did they actually open up to the other about problems they had.
"Where do we go from here?" Jack asked eventually breaking the silence.
"Maybe Martha is right and we should just end it," the Doctor whispered.
"Is that what you want?" Jack questioned him. The Doctor shook his head no.
"No, but I don't know how to fix this," the Doctor replied.
"Me either but I am willing to try to figure it out if you are because I meant what I said. I miss having you as a friend and even if we don't work out as lovers I would still like that part of our relationship to continue," Jack advised him.
"Me too," the Doctor agreed. "I will talk to Martha in the morning about moving in with her and Mickey while I continue to recover."
"You don't have to move out Doc. There is still plenty of space for you at our home. I will sleep on the couch tonight and in the morning I will get a bed and wardrobe for my office. We can figure out the rest as we go but I know you don't want to be away from Emily anymore than you have to and I want you there for her. If it doesn't work, then I will help you move out at any time that you ask or allow you to leave on the TARDIS if you are ready," Jack informed him.
"All right," the Doctor agreed.
"Then I don't know about you but I just want to get out of here and go home," Jack told him. The Doctor nodded his agreement as he really just wanted to lay down for a while and think. Jack put the whiskey away then stood up grabbing his coat and handing the Doctor his. The Doctor pulled it on before following Jack out of Torchwood to the SUV. The ride home was quiet and as soon as they were home the Doctor headed straight up the stairs to lay down. He could still hear Jack moving around the house and the clink of glass as Jack poured himself another drink. It was familiar and comforting despite the heartache that he was feeling over another failed relationship. Curling into himself he pulled his coat over his body as a blanket as he wondered if he would ever be allowed to be happy again.