The Vortex had been unstable for the past couple of hours; there were lots of loud banging noises and flashing outside the TARDIS' windows.
"This is completely normal," the Doctor assured Amy as the TARDIS vibrated uncontrollably for a minute. After running around the console while trying not to fall down and pressing what seemed to Amy like a bunch of random buttons, the Doctor sent Amy to her room with a "Go to bed Pond." She obeyed because she was too tired to argue with him that she wasn't a child and that he couldn't just send her to her room whenever he felt like it.
After being shaken awake by another mysterious vibration running through the TARDIS, Amy Pond ran into the console room after another particularly loud 'bang' only to see the Doctor standing around the console like nothing had happened. "What was that noise?"
"I told you Pond, there are sometimes Storms within the Vortex. Ions get charged and angry, and produce lightning just like on Earth. Loud noises can occur too. Except not really. I should really check that out. Everything is under control I can assure you of that. Not scared are you?"
"No" Amy answered a little too quickly as she tried to shrug it off like it was no big deal. "Why would I be scared?"
"I don't know," the Doctor said exasperatedly. "You humans tend to be scared of strange happenings in the sky or in this case, the Time Vortex. Although sometimes you should be scared because strange happenings can also be very bad happenings. Whatever the strange happening though, I don't believe you. I think you are scared Pond."
"And why would you think that Doctor?" Although she loved that the Doctor was the only person who knew so much about her, she hated that he could read her like one of the books in his library. It was weird to have someone who knew her so well.
"You came running into the console room like a child at the sound of one of the very loud 'Bangs'. There has to be something bothering you. And I will not take no for an answer Pond."
Amy leaned against the console and looked down at the glass floor. "I've never really liked storms." She spoke quietly with a hint of awkwardness in her voice. "My Aunt would always leave me alone in my house. When it would storm the noises and flashes of light would scare me. I would always hide underneath my blankets and cover my ears so I wouldn't hear or see anything."
The Doctor was silent for a minute after Amy's confession. "You're scared of storms, but you weren't afraid of a strange man dropping out of the sky and crash landing in your backyard?" The Doctor asked, obviously confused with his companion's logic.
Another rumble of 'thunder' was so loud that it shook the TARDIS. Amy grabbed on to the console and screamed. The Doctor ran over to her and grabbed her arm in a very friendly I'm-going-to-comfort-you-because-you're-scared-way.
Amy looked up at her Doctor, despite the obvious look of horror on her face, she portrayed to him that she thought the answer to her question was obvious. "You weren't scary. You were never scary. Just a little strange." Amy remembered. Her brows un-scrunched and her expression softened a bit, the memories of her Raggedy Doctor making her feel less afraid. "For some reason I felt safe with you. I was happy to have a friend."
The Doctor didn't know how to respond to her. He was dangerous. The monsters generally found him and he was always in trouble. He was a time traveler, which had the word 'danger' and 'trouble' written all over it. His Amy Pond was always full of surprises. She never made any sense, but that's what he loved about her. Mad and impossible just like him. He lessened his grip on her arm and pulled her into a giant hug—one he didn't seem to keen of letting go of which surprised Amy a little bit. The Doctor wasn't usually one for physical affection.
"That hasn't changed you know," Amy whispered in his ear. "I always feel safe with you."
Her words of confidence and absolute trust in him made him feel a little guilty because mere days ago she watched her fiancée die and then get erased from history. The worst part is she didn't remember it at all. 'Safe' generally wasn't the word he would use to describe life aboard the TARDIS.
The Doctor pushed his guilt aside though and tried to take in this gorgeous and impossible red headed girl that was in his arms and holding on to him like her life depended on it. Another rumble shook the TARDIS but he held on to her even tighter just to assure her that he wasn't going anywhere, not at this point anyway. He placed a kiss on her forehead, like he usually did when she's scared or being magnificent. This time though it was for reassurance: both for his sake and for hers.
He may sometimes leave her, never really on purpose, it's usually an accident; but he will always go back for her because she's his Amelia and he's her Doctor.