An alternative scene for Season 2 episode 3: The Nightmare begins. Spoilers.
Morgana stood there in her night gown looking almost hysterical, waiting for him to say something. She had just told him that she had magic and Merlin wasn't sure what he should do. Should he brush her comment aside and say it was her imagination? It didn't seem right to. She just needed to know that she wasn't going insane.
He knew Gaius didn't think Morgana finding out about her powers was a good idea but maybe Gaius was wrong. "You have magic. I know your scared, I can relate."
She stared at him confused and still scared. "How can you possibly relate?"
Merlin took a deep breath. He knew that there were so many risks with telling her but she had risked so much too by telling him. She needed to know that she wasn't alone in this. "I have magic too."
Morgana eyed him suspiciously. "Prove it."
Merlin looked around half expecting Uther to suddenly burst into the room and then he spotted a candle. His eyes glowed gold and he lighted the candle, shaping the flames into a dragon before his eyes glowed gold again and he put out the tiny flame.
"Can you teach me?" Morgana asked.
"Well I'm still learning myself and-" there was so much hope now in Morgana's eyes and Merlin found himself saying "Yes I can teach you."
Morgana walked over to Merlin and hugged him tightly. "Oh thank you Merlin! Thank you!" Then she let him go and said "So when do we start?"
Merlin scratched his head. "I'm not sure, we'd need to find a place where Uther wouldn't be likely to find us first. Just try to get some sleep for tonight."
Morgana smiled at Merlin. "Thank you." Right before she left she looked back at Merlin and added "Your secret is safe, you can trust me Merlin."
"You can trust me too," Merlin replied. "Good night my lady."
"Good night Merlin." After she left Merlin let out a sigh. He knew that he was doing the right thing but he couldn't help but wonder what he was getting himself into.