This missing scene begins after the end of Season 3, Episode 1 - "The Birthday"...
It took all of Damon's self control to walk away from Elena while he was so angry. Not that he would ever intentionally hurt her, but he didn't want her to see him this way - she had seen him at his worst far too often before.
She had found out that he had been tracking Stefan and Klaus, something he had hoped to keep from her until he had dealt with them himself. Now though, things had changed.
He found himself surprised by the anger he felt at Stefan over what his brother had done to Andie. He had felt no such emotion when he saw the other deaths Stefan had caused, the other things his brother had done. Somehow, Andie was different.
Damon knew that Stefan was targeting him. He had said so, and he had done it in the only way possible - the only way possible except for hurting Elena.
He wasn't sure Stefan would ever be so far gone as to hurt Elena physically, but it was something to consider, something to prevent.
The pain from what happened to Andie was bad enough, then Elena had been there when he returned home, confronting him, challenging him. He hadn't meant to tell her the truth the way it had happened - he hadn't meant to tell her this at all. She had lost so much, he didn't want her to lose hope as well.
Still, he should have realized he couldn't keep this from her. This or the feelings he still had for her, but hadn't expressed for some time.
He didn't want to think about the feelings just now, but now she knew about Stefan. Now he was sure his worst nightmare would come true. Now she would insist on finding Stefan. She was already in denial to some extent, not believing that "her" Stefan could do what he had done.
Maybe she would eventually realize what Stefan really was now, but it wouldn't matter. She would still insist on finding him and trying to fix him. And it would be up to Damon to help and protect her.
Elena knew that, under any other circumstance, a call with no voice from the other end would be creepy. Creepy or worse. She wasn't sure why she thought it was Stefan, maybe it was just hope. Damon had just told her that Stefan was alive, though he had said other things she wanted to deny. Still, if he was alive, if the call really was from him, there really was hope.
She held onto the phone long after the call ended. She held onto it as she lay in her bed reliving her birthday.
Elena's birthday had turned into a day of disaster. First, Jeremy was using again. She had no idea what to do about that, but she had hoped Alaric would.
Then Alaric had left. She wanted him to stay, she had tried to tell him as much without actually saying it, but it hadn't worked. He had done so much for her, had stayed with them for so long that she couldn't bring herself to ask for any more from him - no matter how much she wanted it.
Finally, worst of all, Damon had been hiding things from her - telling her that the leads they were following were dead ends when he had actually been tracking Stefan.
She felt betrayed by Damon. She knew he was helping her, she knew he would do anything she asked, so she tried to not ask for too much from him. Still, she had thought they were on the same side on this, on finding Stefan. Now she learns that he had kept her out of the loop.
She assumed he was just trying to protect her - he always had and always would. She may have denied it when Damon told her that it was Stefan causing the vampire-related deaths they were hearing about, but she knew what Stefan had been like when he drank human blood. Stefan had told her himself, she had seen it herself when she let him drink from her when he needed to. That time, she had been able to fix him, bring him back to normal. Well, she and Damon had been able to do it.
Her mind went back to the times Damon had helped her. She knew he loved her - not that he had mentioned that recently. Neither of them brought up the kiss she had given him when she thought he was dying. She simply told those few friends that knew about it that she it had been a "goodbye" kiss because she thought he was dying. It seem to satisfy her friends, but Elena knew better.
The feelings she felt as she listened to Damon's death-bed confession, as she accepted him and as she kissed him, were strong, strong enough that she hadn't forgotten them. She doubted she ever would forget them. She still felt them sometimes when she and Damon were together. She tried to hide them, maybe she did hide them, but she still felt them. And they were as strong as ever.
Elena knew that Damon loved her, he hadn't even tried to to hide it before the bite, before Stefan was gone. Yet he hadn't said anything like that since his recovery. Maybe it was because Andie was back in his life, maybe it was becuase she didn't mention it at all herself, or maybe it was because he was hiding more from her than just his tracking of Stefan. Maybe he was hidings the feelings for her he had so freely expressed before.
She wasn't sure why he would do that, especially after they had opened up to each other on what they had thought was his deathbed. Of course, she wasn't sure why she was avoiding the subject either. She just couldn't bring herself to face the feelings just yet. And for whatever reason, he was giving her space, so she was taking it.
Really, it was confusing to Elena. Finally, the long awaited hope for Stefan, yet the feelings for Damon wouldn't go away.
She would look for Stefan, Damon would help her. That much she was sure of, even though she also knew that for her, and she suspected, for Damon, the feelings between them were still there. They were still there and she knew she wouldn't be able to deny them forever.
Sadly, it appears Elena is still lying to herself. It appears this little game must continue. I'm not sure if I should be happy about that, or if I should just cry about it. I guess it doesn't matter - we can't expect the show to get everything right. There are missing scenes to be written, and, for as long as necessary, I will write them...