Time had just been rewritten and the Doctor had fought against it in a way that he had done only very few times before. He had faced fixed points quite a number of times but it wasn't often that he was forced to fight future versions of himself or his companions. As Clara went for a swim in the Doctor's massive swimming pool, the Time Lord cleared up the control room of the TARDIS which was still grumbling about her experience with the salvage team. The Doctor vaguely wondered what had happened to the van Baalen brothers but he didn't really care; he was too busy thinking about Clara.
The girl had lived at least three lives, four if he included her alternate counterpart being turned into a Time Zombie, but she had absolutely no idea of what had happened to her. The Doctor felt slightly guilty for ever being suspicious of her. Whatever had been done to her, Clara knew nothing about it and if her apparent immortality had been caused by something evil, it meant she was a victim not an accomplice. The Doctor remembered when they had stood on the edge of the cliff in the TARDIS and he had yelled accusations at her. She had looked so scared and confused that he could hardly believe he had ever thought she was an enemy. He wondered if her apparent immortality might actually be a good thing; of all his still living companions only Jack Harkness had a lifespan that could potentially exceed his own, but if Clara kept popping up anywhere in Time and Space he could potentially have a companion for the rest of his life. The Doctor hadn't felt this happy since Victorian Clara had showed him that life was still worth living.
Clara would have no memories of the days events, but the Doctor promised himself that he would do his best to treat her better from now on. Until today he hadn't really thought of her as a person, even though she had told him twice that she didn't want to be compared to a ghost. He had just considered her a puzzle and he was angry with himself for ever thinking of her that way. Yes she was mysterious but she was still as human as Amy or Rory or any of his other human companions.
Clara appeared in the room with wet hair and a towel over her shoulder, having just climbed out of the swimming pool. The Doctor had been so distracted trying to unravel the mystery around her that he had never truly realised how beautiful she was. She climbed the stairs, without her usual energy and slumped on the console.
"I feel exhausted," she confessed.
"We've just had two days crammed into the space of one," the Doctor said moving around the console. He had a good view of Clara's bottom from his position and remembered when her Victorian incarnation had told him to climb a ladder first so he couldn't see up her dress. Before he could stop himself, the Doctor slapped Clara's bottom with the towel. Clara either didn't mind or was too tired to notice.
"Why would you say that?" asked Clara and the Doctor remembered that she was not Amy or River and therefore couldn't remember alternate timelines.
"I dunno," he said, "I say stuff." Clara smiled and then moved towards the stairs, "Do you feel safe?"
"Course," she replied cheerfully. The Doctor wondered if she was hiding her emotions; she was good at that.
"Give me a number out of ten," he said spinning to face her, "Ten being woo hoo, one being aah!"
"You're being weird," Clara informed him.
"I need to know if you feel safe," the Doctor said, remembering the horrible fates of Oswin, Victorian Clara and most recently Clara's Time Zombie counterpart. He had a feeling that Clara's alternate future self, as well as those of himself and the van Baalen brothers, had just been begging for help rather than intending harm but the fact that they couldn't speak and burned anything they touched meant that there was nothing he could do for them. It was possibly even worse than being turned into a Dalek and he thanked the Universe that he had been able to stop it from happening, "I need to know you're not afraid."
"Of?" Clara asked.
"The future," said the Doctor and looked into her beautiful brown eyes, "Running away with a spaceman in a box, anything could happen to you."
"That's what I'm counting on," Clara replied then nodded towards the console, "Push the button." She smiled at him and then went down the stairs. The Doctor watched her leave with a smile on his face. Until today he had taken Clara for granted and frankly he had repaid her loyalty with suspicion and even hostility but now he realised how lucky he was to have her. He promised himself that he would not let her die a fourth time. Even if he had to regenerate, or actually die, in order to protect her, he would not let anyone harm her. Clara's mystery would reveal itself in time. The Doctor decided that instead of looking for the answer, he would wait for it to come to him.
For now he and Clara would run together through time and space.