They made it to the hub early the next day as everyone was awake and ready to go. The Doctor had briefly gone on to the TARDIS that morning causing Jack to worry that he was going to have to drag him out but he returned just as quickly with a smile on his face. He didn't complain as Jack helped him into his coat climbing into the back of the SUV without a fight. Suspicious, but thankful the Doctor was being cooperative, Jack drove them over to the hub. Upon parking in the Plas, the Doctor jumped out running across the pavement.
"Stop running," Jack called after him. The Doctor was still supposed to be taking it easy after his procedure. The Doctor didn't listen as he took off into the hub with Artemis on his heels. Jack shook his head as he headed at a normal pace into the hub after him. It was obvious to him that the Doctor wasn't afraid or in pain, so he saw no reason to chase him. Despite Jack yelling at him, the Doctor didn't stop running as he made his way through the hub and down the stairs. He ran into the archive room stopping when he saw John sitting in his normal spot.
"Hello, Doctor," John told him pleasantly.
"Here," the Doctor responded. He reached into his pocket pulling out a long thin silver rod with a blue light on the end. John reached out taking the sonic screwdriver from him.
"But this is yours," John stated. The Doctor shook his head no as he pulled out a second sonic from his pocket.
"This Doctors," he replied. He flipped it in the air missing it. John caught it for him. He held it out to him and the Doctor took it with a smile. He quickly shoved it back in his pocket. The smile faded as he looked at John seriously. His next words were soft and slow as he made himself clear. "She said she forgives you."
"Who forgives me?" John questioned in confusion.
"The TARDIS," The Doctor answered his words quick again and happy. He bounced a little on his heels obviously excited about something. John nodded his understanding as he watched the Time Lord. Their two TARDIS's would have connected the moment they were close to each other, sharing information between them. His own TARDIS was linked to him and knew the pain he carried over the loss of Rose. She had comforted him for many hours as he sat in her console room, not sure what else to do. In his heart, he knew that he should have been with his family, but he couldn't face them at the time.
"I'd like to see her. That is when Jack says it is alright," John suggested.
"Yeah," the Doctor agreed. He looked towards the door as Jack entered. Smiling, he flung himself into the Captain's arms. Jack caught him, smiling as well. He was pleased the Doctor was in a good mood and his smile was contagious. He kissed the Doctor on the side of the head and the Doctor turned his head. Jack caught his lips briefly in what was obviously an attempt at a chaste kiss. The Doctor wasn't having it and he attempted to deepen the kiss. Jack pulled away with another gentle kiss.
"Later," he informed the eager Time Lord.
"Fine," The Doctor sighed.
"You're having sex with him," John stated the disgust in his voice clear. The Captain he knew would sleep with any man, woman, plant, or other alien-like creature. He had suspected it when he first saw them in London together. As he watched the Doctor, though, he began to question his first assumption even if he planned on getting the Doctor away from Torchwood. Normally, them sleeping together wouldn't have surprised him. It was the fact that he was sleeping with the Doctor while he had the brain capacity of a child is what disgusted him.
"No," Jack immediately answered as at the same time the Doctor responded. "Yes," causing Jack to sign. He continued on as John stared at him. "Fine, we are having sex but not in the way you are thinking. I swear to you, I am not hurting him or doing anything that he is uncomfortable with."
"Does Martha know?" John wondered.
"Yes, and while she may not completely approve, she does understand," Jack stated. "Ianto also knows and encourages our relationship. The rest of my team hasn't asked and frankly, it is none of their business or yours about what I do in my personal life."
"Fair enough," John responded not questioning it further. Even if he was disgusted if Martha understood and Ianto approved, then Jack was right and it was none of his business.
"So I was going to wait to have this conversation later when you were with Martha and I in our meeting, but since I am here I want to know if you found out anything from the tests that you ran," Jack questioned. He needed to know that the tests actually had produced a result and that they had hurt the Doctor for nothing.
"I have. While the blood and urine tests didn't tell me anything new, I did find an unusual enzyme in his spinal fluid. Further research, has revealed that it is caused by a neural inhibitor that they would have surgically implanted during his incarnation," John stated. He had given up on finding anything in the samples that he had received. Giving up, he had instead started to look for a way to remove the energy from Donna and open up her mind to him again. He wasn't sure that he could actually find a solution but he had hope that he could speak to her again. It was after the exhaustion overtook him and he started to drift off to sleep that the problem with the Doctor's telepathic barriers began to bother him. Returning to the archives, he once more began working with the spinal fluid until he found what he knew would be there.
"What is a neural inhibitor?" Jack questioned trying not to get his hopes up.
"It is a small metallic device that is inserted at the base of the brain. It can be used for many things but the most common use is to block the telepathic centers of the brain rendering them almost useless. It would prevent the Doctor from any psychic attacks, it would also keep him from building a wall to protect his mind and from communicating with his TARDIS properly," John explained.
"Can it be removed?" Jack wondered. John shrugged.
"We would need to x-ray his head to find the location. It also depends on how it is attached to his brain. I will be honest with you Jack, that I have never heard of one of the implants being removed before. Mainly because all of the test subjects died before they could be," John answered. Jack looked at the Time Lord in his arms. He wasn't listening to the conversation as he bounced a little on his heels, obviously getting impatient. Jack kissed him on the top of the head.
"Then he will be the first," Jack told him confidantly.