These missing scenes begin near the end of season 2, episode 9 - Katerina, where Stefan and Elena are on her porch, hugging...

Stefan

He let her hug him and cry until she was done. He was willing to let it go on for as long as she needed. He tried to think of something comforting to say, but nothing he tried before had worked. He doubted anything would.

The sobs had stopped when he said "She could be lying, Elena."

Elena pulled herself from him and shook her head. "Everything she did makes sense now, Stefan. Everything."

"That doesn't make it true."

"Or false, Stefan," Elena closed her eyes and rubbed her head with her hand. The tears were gone but the stress remained. "I don't know what to do."

Stefan tried to touch her face with his hand, but she backed away from him. "I'll protect you Elena. I told you, I won't let anything happen to you."

"You can't. Everything she said is true."

"No Elena," Stefan said, trying to touch her again. She let him. "She said she came back for me. It was a lie."

"Why do you say that? Because she wouldn't really want you? I do." Elena backed up until she was against the door and shook her head. "She could have come for the other things and want you as well. Maybe I am just like her."

"You're nothing like her, Elena." Stefan looked desperate. "She has done nothing but hurt people since I've know her."

Elena stared at him. "You mean since you found out she wasn't dead or rotting in a tomb. Before then, you loved her," she accused.

Stefan hesitated, trying to think of a response.

"She did what she had to to stay alive. Maybe I would have too."

"No, Elena." Stefan contradicted, shaking his head. "You're not like that at all."

"Aren't I?" Elena asked softly. She almost looked resigned."When I thought it would keep me and my family alive, I broke up with you. I hurt you, even though I love you. Not someone who was trying to kill me, not someone I didn't know. I hurt you. How different is that from what she's done?"

She turned and opened the door to enter.

"Elena, are you OK?" Stefan asked desperately. "Are we OK?"

Elena shrugged as she looked back at him. "Maybe. I want us to be, you want us to be. Maybe." She entered, closing the door to him.

Damon

Damon was outside as she exited her home the next morning.

"What are you doing now, Damon?" Elena asked, sighing.

"Making sure you get to school." Damon said, his face blank. "I hear you've been skipping."

"I had a reason." Elena said under her breath.

"Yes. I heard you talked to the bitch."

"Don't call her that. She has a name." Elena retorted.

Damon's face showed a little surprise. "A name and a new BFF?"

"I just understand a little about what she's been through," Elena said quietly.

Damon almost glared back. "It doesn't make it OK for her to try to kill you."

Elena lowered her eyes and spoke softly. "I know. But at least I learned why she was doing what she did."

"And why is that, Elena?"

"She's trying to stay alive," she replied, looking at him again. "If she can give Klaus a vampire, a werewolf, a witch, the moonstone and me, she thinks he'll let her live."

Damon smirked. "See any flaws in this plan of hers, Elena?"

Elena frowned and shook her head.

"Klaus is an ass. As a first-class ass myself, I know that you don't leave people alone just because they give you what you want, epecially after they kept it from you for 500 years."

Elena's frown slowly turned to a look of desperation. "I can't do anything to stop him. If I run, he'll destroy my family and everyone I love. If stay, he'll kill me, Caroline, Tyler and Bonnie." She closed her eyes and shook her head. "I don't know what to do."

Damon gently pulled her chin up. She looked into his eyes as he spoke. "Where's the Elena that ran into a house full of vampires to get Stefan? The Elena that ran into a tomb full of vampires for me? That faced me while she was bleeding and dressed me down because of what I did to Vicki?"

"This is different," Elena said softly. "I don't know what to do."

"It is different," Damon confirmed, almost whispering. "This time you're afraid. You don't need to be, you're not alone."

"He'll kill you. He'll kill everyone."

Damon laughed slightly. "He may try. Maybe he is after Caroline, Tyler and Bonnie. He's after Rose too, and since Stefan and I took you from an Original, I'm sure he's after us as well." Damon's face became hard. "But we're not running, Elena. He's not getting us and he's not getting you."

"Why would you try to fight him?" Elena asked desperately. "Katherine ran, Rose ran. Why not all of you?"

Damon's face remained hard. "Because he pissed me off when he took you. He's trying to hurt someone I care about, someone all of us care about. No running and no giving him what he wants. He'll get his werewolf, his witch and his vampires – he'll get to fight us. He won't get you."

Elena closed her eyes and rubbed her head. "God, I can't do anything. I don't know what to do."

"Go to school, Elena."

She looked back into his eyes. "What are you going to do?"

"I'm going to find a way to put an end to it. Got a tip that we might be able to use the moonstone to put an end to this."

Elena stared. "Katherine said…" she started, then began to shake her head. "You can't…"

"Go to school, Elena." Damon interrupted. "You need to, you're not dying and no one's running. Go to school."

Elena stared at him as she backed away from him a couple of steps before whispering "Be careful" as she turned around and walked away from him.