Disclaimer: In case this FanFic seems really familiar to any of you, yes I have permission to use parts of hiholly123's story "Only the Beginning". So don't report me for something I have already asked permission for. Thanks. I don't own Doctor Who or Avengers.

WARNING: May contain some language and other things not suitable for people 13 or younger.

Prologue:

I had left my brilliant Ponds. I had said good-bye to Craig, but more importantly, I had left my Ponds. I sighed and stroked the console hearing a hum of comfort.

"Thank you Sexy," I said, smiling sadly.

She hummed again and flashed the lights softly. I sigh again and lean against the console. Thinking back to all of the adventures I had with my Ponds and all of my other companions, I smile sadly, thinking about all of my failed attempts to protect them. I felt something drip on my hand and looked down. To my surprise, I was crying. I laughed bitterly and wiped the tears away. My thoughts then drifted to my last face and the events leading to my regeneration into this face.

I was forcefully thrown from my dark thoughts when the console room suddenly tilted sideways. I was thrown around the room like a rag doll and slammed hard into the railing. The air leaving my body in a whoosh of air. I gasped for breath and was then thrown again, this time hitting my head on the edge of the console knocking me unconscious.

*TIME SKIP*

I woke up approximately three hours, forty-three minutes and twelve seconds later and found the TARDIS silent and dark, only the backup generators were on. Trying to sit up, I fell back down with a sharp cry of pain as my ribs and head immediately protested my movement. I lay still taking stock of my injuries, which included three broken ribs, a concussion and a stress fracture in my left ankle. After finally getting my breathing under control, I sat up slowly wincing in pain the whole way.

Slowly, I became aware of people shouting something through the TARDIS door. Crawling toward the door, my vision tilted making me nauseous. Finally, I made it to the door and pulled myself into a standing position, making sure that I didn't put too much pressure on my fractured ankle. I swayed dangerously, tilting to the side my hand shot out for balance. I winced, my head throbbing along with my heartbeats and the pounding on the door. I pulled myself up from my slouched position, fixed my bow tie and plastered the most fake smile on my face and then opened the door.

When you hear an ominous clicking noise it's safe to say that you are in a lot of trouble, especially when that clicking noise is of the safety's being turned off on guns. I slowly raised my hands in the universal sign for surrender and stepped the rest of the way out of the TARDIS. The first thing I noticed were four guns pointed in my direction. The second thing I notice is that I seemed to have landed on a ship of some sort.

"Who are you?" a gruff voice demanded.

I turned to look at who spoke and I saw a dark-skinned man who looked like a pirate. I smiled and said, "Just someone traveling through. I mean no harm, so if I'll be on my way- " I tried to move back into my ship, but the guns clicked again, signaling that they were not going to let me go so easily.

"I'll only ask this once more," the pirate said, "Who are you?"

I sighed, but then winced slightly when a sharp pain shoots through my ribs.

"I'm the Doctor," I said.

"Doctor who?" another man asked. He was standing slightly behind the pirate and wearing a suit that reminded me of one of the guys on the movie MIB.

I grimaced at that, remembering everyone who ever said that to me.

The pirate looked at MIB guy and nodded. That must have been a signal because he and two others stepped forward cautiously, guns still pointing at me and when they came within reaching distance, the two others put their guns in their holsters and reached forward and grabbed my arms, putting them into some kind of handcuffs behind my back.

The jerking motion of my arms being forced behind my back caused my ribs to protest loudly. I hissed loudly in pain. Dark spots filled my eyes and I blinked rapidly, trying to push the spots away.

The guards hesitated for a brief moment, but they then just continued on like nothing had happened. They practically dragged me to a room that had some sort of glass cage in the middle of the room. I stumbled and was roughly pushed inside, I instantly fell to the floor from the momentum. I cursed loudly in Gallifreyan as my ribs met the metal floor.

Pirate man looked at me stoically while MIB guy and another man with a bow looked at me with hidden sympathy. I didn't care, I was too busy trying not to let the pain drag me under. My breathing was very heavy and I could barely breathe, the darkness in my vision threatened to pull me under but I fought it back. For now, at least.

I stood up slowly, gritting my teeth, with my hand wrapped around my ribs and my eyes squeezed shut tightly in pain. The pirate who was now the only one left out of the three, watched me as I stood, his one eye not leaving me. He just stood there with his arms crossed. Standing up straight, I kept my weight off of my ankle and stood there, hunched over slightly.

"Sooo…. Is this going to be an interrogation?" I asked with as much bravado as I could muster. Which at this point was not a lot. "Because if so, this is the worst one I have experienced so far, and I've been in a lot of interrogation's."

"This is not an interrogation. Well, at least it won't be if you answer my questions," pirate said.

"I'm sorry, I'm afraid I don't know who you are or where I am," I said as politely as I could while still trying to not pass out.

"I am Nick Fury, Director of S.H.I.E.L.D. You are on our Helicarrier, and since I'm assuming you're some kind of alien life form, seeing as you arrived in some kind of ship, you are on planet Earth," he said, like he had this type of conversation all the time.

"I always have to end up on Earth don't I," I said quietly to myself.

"What are you and where do you come from?" Fury snapped impatiently.

I laughed bitterly and said, "I am a Time Lord from the planet Gallifrey."

"Are there any more of you out there that I should be concerned about?" he demanded.

As soon as he asked that question, my mind flashed back to the days of the Time War and how everyone had died and how there was no other choice but to destroy my home planet and the Daleks along with it.

"No. There is no one else out there. I am the last of my kind," I said, pain coating my voice.

Before Fury could ask any more questions, MIB guy came back into the room and whispered something in his ear. Fury nodded and said, "Bring them up and call Thor while you're at it."

MIB guy nodded and left. I then realized what Fury had said and I started panicking. The last time I saw Thor had been right after I ended the Time War, and he had been so furious at me, that he had tried to kill me.

"I'm sorry, did you just say Thor?" I asked shakily. My vision was starting to turn dark.

Fury just looked at me confused and he didn't answer. My breathing picked up and the pain became too much for me to handle. I then fell onto the floor and I heard someone shouting something. The darkness then swallowed me whole and I drifted away.

To be continued…

A/N: Hope you guys liked the first chapter. I will hopefully update once a week for you guys. Please review it helps me out, just don't be mean about it. Constructive criticism only. Thanks.