Years passed. The Doctor stayed less and less time at the Hub and traveled the universe again. He still had trouble with keeping control and he made a mistake on Mars. He had retreated to the hub afterwards and hid from them. He refused to talk about what happened only saying that he had changed time. One morning they woke to hear the sound of the TARDIS leaving.
When he returned again his body was burning up and he was crying he didn't want to go. The regeneration energy danced across his skin and he fought it. Martha tried to comfort him and tell him that it would be okay, but he cried and clung to Jack. He fought the regeneration for so long that Martha was worried he would die before it actually happened. She cooled his body with bags of ice and helped him hold it back as long as he could. When he couldn't any longer, he went into the safety of the TARDIS.
They saw him again later that day. His mind was clearer then it had been in a long time, but he was klutzier and lankier. Jack had laughed at his new clothes and the way he proclaimed his bow tie was cool. He told them all about the little girl named Amelia Pond, who was now Amy. He didn't like her new name, it wasn't a fairy tale name. He agreed to continue having regular check up's with Martha but insisted that he didn't need them anymore.
He kept his promise for awhile though. He showed up at the agreed upon times or when he was particularly distressed. He complained often about a woman named River Song. Martha had laughed at that, while Jack had silently let the Doctor go again. The visits stopped for a while and both of them worried that he had forgotten them.
Ianto married Sky. Martha and Mickey settled down together and had two sons. Jack though had became obsessed with finding the base that had held the Doctor and chased lead after lead. He came away empty handed more often than not. But he was still determined. He was getting ready to leave again, when his phone rang and he almost didn't answer it.
"Hello?" He asked impatiently.
"Jack, what do you know about Demon's Run?" The Doctor asked.
"You found them." Jack sat up in surprise. "You have to take me there."
"I all ready took down the base." He replied. "It's over Jack, it's time for you to move on." The line went dead and Jack stared at the phone. He had been fighting for answers for so long now, he wasn't sure what else to do. He returned to the hub and hid in his work. He spent day and night tracking down things that came through the rift and making Cardiff safe. He waited for the Doctor to return to refuel. He wanted to see him one last time. He knew from the Doctor's words that it would be awhile, but that was okay, he had eternity.