These missing scenes begin near the end season 5, episode 1 - I Know What You Did Last Summer...

Elena

It hurt every time Elena did it, every time she told Damon that she loved him over the phone.

Really, she hadn't had to do it often. The first time was when she had been compelled to leave him. That seemed like such a long time ago. Even then he was taking care of Jeremy for her. The circumstances were better this time, she could go to him if she wanted. This time, she had left on her own, gone to school away from Damon and her brother. Living with Caroline wasn't ideal, as soon as they were out of the car, the blonde vampire was dissing her relationship with Damon again, calling her breakup with Stefan a mistake. It wasn't that great a start for her college experience.

But Elena was able to get through it, and her feelings about Damon during this separation only confirmed the truth. The sire bond may have been gone, but the feelings for Damon were still there, and they were as strong as ever.

She was a little annoyed when Caroline talked about Damon, but it wasn't hard to ignore - even before Megan had fallen dead at their feet. Even before she heard Caroline crying over Tyler's deciding not to come to school with them.

Now she could only feel pity for the vampire that had betrayed her trust more than once, the vampire that Damon had gone to save more than once.

As tempting as it was to go back to Damon, Elena was staying with Caroline. Not that it was the pity she felt for the blonde vampire, it was the mystery of Megan. She didn't know if the girl was an innocent or not, but she knew that the girl was tied to her father. He seemed to have trusted her, and that got Elena's attention.

Though she was resolved to stay in school with Caroline, she was starting to wonder if it had been such a good idea to share whatever was going on in her mind about Stefan. It wasn't dreaming, like Caroline kept calling it, but it was something, and it worried her.

She was sure, though, that whatever it was, Damon would help her figure it out. And, if needed, he would go wherever she needed to go with her. But this time, at least, if they needed to go somewhere to resolve the Stefan issue, she wouldn't have to hide her feelings for Damon.

Damon

Damon couldn't believe what he had done - hugging Jeremy. It had been an impulse; and really, it was as close as he could get to Elena just then. But thinking about it made him cringe a little.

So he resolved not to think about it.

It was easy to not think about it, all he had to do was think about what Elena had told him. He had asked if she wanted to come back to him, but he was just as tempted to go to her. In their brief history together, in the time since he had become convinced that she really did want to be with him, their separations had always been like this. They had always had really bad days at the same time. He always found out over the phone how bad her day had been.

But they had always been able to work through it.

She was staying in school. It was what she wanted, so he was going to do everything he could to make sure she could stay - including making sure Jeremy was becoming what she wanted.

Jeremy was talking again, so he looked in that direction. Elena's brother looked pretty much normal now.

"I'm a hunter," Jeremy was saying, "but I keep being saved by vampires. First Elena, now you."

"Quit dying," Damon retorted, "and we'll stop. Elena would love it if you could go for a year without..."

Damon cut himself off and tilted his head, annoyed. Jeremy wasn't looking at him.
But the hunter's expression was changing. He was starting to shake his head.

"Bon..." Jeremy began, and then he looked like he was reaching for someone.

Damon was about to say something when Jeremy suddenly turned back to him. "We need to find Katherine.

"Find her?" Damon asked sharply. "Why?" He would have thought that Jeremy would be glad to be rid of the vampire-turned-human.

"Because Silas wants her." Jeremy said, turning away to begin the search. "Because wherever she is, he will go. And because as much as I want to kill all vampires who are not my sister, I want him dead."

"Isn't he supposed to be immortal," Damon asked Jeremy's retreating figure. "You're not supposed to be able to kill him, and how do you know this anyway?"

Jeremy stopped briefly and looked back at Damon. "I'm a hunter. I know things, and you have no idea what I can do."

Damon shook his head and moved to follow knowing that whatever Jeremy was doing, Elena would want Damon to be with him.