I do not own Doctor Who, Agents of Shield, Agent Carter, the Avengers, or Guardians of the Galaxy. Only this story. This story contains spoilers for Doctor Who S8, Agents of Shield S2, and Avengers 2: Age of Ultron. Read at your own risk. This is also a sequel to my first story "The Fight for Earth". It is suggested that you read that before continuing. Also there aren't many Marvel characters in the first few chapters, but I promise more will be appearing after that. In fact, there will be connections to other areas of the Marvel Universe including Agent Carter and Guardians of the Galaxy. I hope you enjoy the story! :)
Chapter 1
New York City, United States 1946
It was 9:00 p.m. as Connie walked down the busy Manhattan streets. The sky over New York was dark at night, but that only made the city glow even brighter. Connie was a young woman on a mission. She was once a friend of Steve Rogers before he became the famous Captain America. However, Steve died before the war was over. It seemed so strange to her that science could change a man the way it changed Steve. So, she began researching advanced science and super human technology. She soon caught the attention of Peggy Carter, a talented secret agent and former love interest of Captain America. The two women had been doing some free lance investigations recently, given that most men in their line of work deemed women as too frail for the dangerous lifestyle of a secret agent. In fact, Peggy and Connie had discovered something strange. They approached American intelligence agencies about what they discovered, but were dismissed. It was assumed that Peggy and Connie had let their imaginations run wild. So, the two women decided to find out for themselves what was going on. However, this was no ordinary human technology. They had reason to believe that what they had discovered may have been of alien origin. There were only two people in New York with extensive experience with aliens: Amy Pond and Rory Williams.
Connie had short, brown hair that she curled (as was the style of the day) and beautiful brown eyes. In fact, she looked exactly like the Doctor's current companion Clara Oswald. Connie was one of Clara's numerous echoes scattered across the universe, yet she was completely unaware of this. Peggy told Connie to meet Amy and Rory and ask them for their help. Connie continued the walk through Manhattan until she came upon an apartment building near Central Park. She calmly walked inside, through the lobby, and up four flights of stairs. Then, Connie came upon a hallway filled with doors. Behind each door lay a different apartment. She walked down the hall and stopped at the fifth door on her right. Connie then knocked on the door. Soon the door opened and a red haired woman was standing there. Connie assumed this woman was Amy Pond.
"What do you want?" Amy asked. "Do you have any idea what time it is?"
"Hello. My name is Connie." She said. "Are you Amy Pond?"
"No one calls me that." She said. "My name is Amelia Williams."
"May I come in Mrs. Williams?" Connie asked. "I've walked a mile through downtown to come and find you."
"No." Amy said. "Tell my why you're here."
"My colleague and I would like your help." Connie said.
"With what?" Amy asked.
"Aliens." Connie said.
Amy stared blankly at Connie for a moment and then said "I don't know what you're talking about."
"Yes you do." Connie said. "So does your husband. May I please come in?"
Amy stepped aside to allow Connie to enter. Amy then shut the door. Connie walked into the living room. Amy and Rory seemed to have a cozy place to live. Soon, Rory entered the room. He'd only been home for about thirty minutes after spending the whole day working at the hospital.
"Who's this?" Rory asked.
"I'm Connie." She said with a smile.
"She says she wants our help with aliens." Amy said.
"There must be some kind of mistake." Rory said.
"Save the act Mr. Williams." Connie said. "My colleague and I know about you both and about your history."
"Prove it." Amy said.
"We know about the Doctor." Connie said.
"Who is your colleague?" Rory asked.
"Agent Peggy Carter." Connie said. "We do a lot of freelance investigating. We'd like your help with a case. It's like nothing we've encountered before."
"How do you know about us and the Doctor?" Amy asked.
"You all pop up throughout history." Connie said. "When you do, people write them down. Vincent Van Gogh wrote about you. Winston Churchill wrote about you. Hitler wrote about you. All these texts have been hidden and locked away, but they can be found if you know where to look. I'm sure you also remember Mercy, Nevada. There's a ninety year old woman there who still remembers what happened with you and the Doctor and the Kahler robots back in 1870."
"What's the problem?" Rory asked. "How do you know it's aliens?"
"We don't." Connie said. "Neither Peggy nor I have encountered them before. That's why we want your input."
"Why didn't this Agent Carter come meet us herself?" Amy asked.
"People in this city know her and they know me. We didn't want to draw too much attention." Connie said. "Would you come with me to the Empire State Building? Peggy is waiting there for us."
"Can't we do it in the morning?" Rory asked.
"I'm afraid not." Connie said. "More people will keep going missing the longer we wait."
"People are going missing?" Amy asked.
"Yes." Connie said. "Peggy will tell you everything when we get to her. Will you come with me?"
"Yes." Amy said.
London, England 2015
It was a sunny morning in London. Martha Jones, Mickey Smith, and Jack Harkness had embarked downtown on their way to U.N.I.T. headquarters in the Shard, London's tallest skyscraper. Martha, Mickey, and Jack were made honorary S.H.I.E.L.D. agents by Nick Fury himself after they helped save the planet from the double invasion of Daleks and Chitauri alongside the Doctor, Clara, River Song, the Avengers, and Agent Coulson's S.H.I.E.L.D. team. However, since it became known that H.Y.D.R.A. had infiltrated S.H.I.E.L.D., the three of them laid low in London, doing what they could to fight H.Y.D.R.A. underground. The previous night, they found Clara Oswald crying on a bench near Big Ben. She had told them that the Doctor took her to the Himalayas in 1992, where he was killed by Zygons. She said that the TARDIS took her home and then disappeared with the Doctor's body still inside. Martha was skeptical of this story. So, Clara said that they could ask U.N.I.T. because every time the TARDIS lands on Earth, U.N.I.T. has a file on it. Martha, having worked at U.N.I.T., knew that they did keep accurate records of the Doctor's visits to Earth. On this day the three of them were walking to U.N.I.T. to confirm or disprove Clara's story that the Doctor was dead.
Unbeknownst to them, it was not Clara Oswald that they had spoken to last night. In fact, it was one of two crafty Zygons based in London, who wanted three time travelers to go to U.N.I.T. for their own purposes. Also unbeknownst to Martha, Mickey, and Jack was that today was a monumental day at U.N.I.T. The Doctor(s) and Clara Oswald recently discovered that Zygons, in order to escape the destruction of their homeworld by the Time War, used Gallifreyen technology to trap themselves in paintings that were now held in the National Gallery. Some Zygons has escaped and were planning on releasing the rest of their species. The Doctor convinced U.N.I.T. and the Zygons to negotiate. After multiple scheduling conflicts, U.N.I.T. and the Zygons who had left the paintings were finally going to conference about what to do next. Martha, Jack, and Mickey walked into U.N.I.T. and found Kate Stewart pacing as she walked through the lobby. Kate stopped when she saw Martha, Mickey and Jack. Confused, she decided to talk to them.
"What are you all doing here?" She asked.
"Hello mam." Martha said. "We need to ask you some questions."
"I don't have time." Kate said. "I've got to begin negotiations with the Zygons in twenty minutes."
"It's about the Doctor." Mickey said.
"Isn't it always?" Kate sarcastically asked. "You'll have to come back some other day."
"He's dead." Jack said.
"Sure he is." Kate said. "Of course he is. Why wouldn't he be? Except for that he isn't. This is not the first time we've been told that the Doctor is dead only to find out that he's been alive and well the whole time."
"Can you check your records?" Martha asked. "The Himalayas. 1992."
"Not today." Kate said. "I'm sorry, but I have to go. I suggest you leave."
Kate the walked away from them. Suddenly, a soldier in a U.N.I.T. uniform came up to them.
"I can help you." He said. "You want to know what happened to the Doctor. Follow me."
"Your boss just told us to leave." Mickey said.
"She is very busy today." The soldier said. "She wants to help, but she does not have time. She would want me to show you."
"Alright then." Martha said. "Let's go."
The soldier led them through the crowded building and into an empty elevator. They rode the elevator all the way to the very bottom floor of the building. They stepped out into an empty hallway with one door at the very end.
"What's down here?" Jack asked.
"The answer to your questions." The soldier said.
They walked down the hall and opened the door. Inside was a small, white room filled with three chairs that one may find in a dentist's operating room. At the end of each chair was a wire that connected to a yellow sphere in the far left corner of the room. However, that was not the most surprising thing in there. There was a man waiting for them. It was the Doctor. However it was not the right Doctor. This was the spikey haired Doctor from his tenth incarnation. However, the Doctor that had helped them stop the Dalek-Chitauri invasion was in his eleventh incarnation.
"Hello." The tenth Doctor said.
"Something's not right." Martha said.
The soldier shut the door once everyone had stepped inside and locked it.
"I told you that's not what he looks like." The soldier said.
"This is how he looked in 1946." The tenth Doctor said.
"No." The soldier said. "It's like this."
The soldier's body then began to morph and twist and reconfigure. Within seconds, the soldier was no longer there. He had metamorphosed into the Doctor in his twelfth incarnation, which Martha, Mickey, and Jack had never seen before.
"How was I supposed to know that?" The tenth Doctor asked.
"Remember the Himalayas in 1992?" The twelfth Doctor asked. "This is what he looked like."
"What's going on here?" Mickey asked.
The two Doctors looked at each other. Then, they both started to morph again. This time, their skin turned dark red. They started to grow slightly taller and suction cups formed over their bodies. They were not humans. Martha Jones, Mickey Smith, and Jack Harkness were now trapped in a room with two evil Zygons.