I do not own Doctor Who or Once Upon a Time. Only this story. Enjoy!
Chapter 1: The Flying Pirate Ship
"Do you still think about him?" Danny Pink asked Clara Oswald as they walked down the hallway of her apartment building together. Danny and Clara just had a pleasant night out to dinner. Danny's question was referring to the Doctor. Clara promised Danny that she stopped traveling with the Doctor, even though this was a lie.
"Sometimes." Clara said as they came to the door to Clara's apartment. "I'm still happy being here on Earth with you."
The couple then shared a goodnight kiss before Clara entered her apartment alone and closed the door behind her. She had a truly wonderful date with Danny. However, Clara's night was far from over. As she walked into the living room and put her purse down on the table, she saw the TARDIS, sitting right in front of the window. Soon, the Doctor stepped out of the TARDIS doors.
"Oh good. You're home." The old Time Lord said. "I found it."
"Found what?" Clara asked.
"The last Eye." He said.
The Doctor was referring to the three Eyes of the Mystic Fates. These were three glass eyeballs. Each eye contained massive amounts of magical power and they were scattered across time and space. The Eye of Life was in Regina's vault in Storybrooke. She acquired it when she was the Evil Queen. The Dark Curse brought it to Storybrooke along with her other magical possessions. The Eye of Death was inside the TARDIS after Clara stole it from Peter Pan back in Neverland. The Eye of Birth was in Oz, but it was sent to an unknown world in the future to keep the Wicked Witch from ever getting her hands on it again. The Doctor was determined to find the Eye of Birth so that no one else could. Not for selfish reasons of course. The Doctor just wanted to be sure that the Daleks, the Cybermen, the Sontarans, or any of his other foes didn't find it.
"Where is it?" Clara asked.
"It's on another a planet. It's a world I've been to a few times before. I went with Rose and Martha." The Doctor said.
Clara remembered Rose and Martha fondly. She hadn't seen them since they fought Peter Pan and the Daleks on Neverland together. Then, Rose went back to her parallel world and Martha went back with Mickey to help fight aliens on Earth with Torchwood.
"Which world?" Clara asked.
"It's called New Earth." The Doctor replied. "Five billion years in the future, the Earth dies and humanity finds a new one. The Eye is somewhere in its largest city."
"Which is?" Clara asked.
"New New York." The Doctor said.
"New New York?" Clara asked.
"Technically it's the fifteenth New York since the original, but it's easier just to say New New York." The Doctor said. "What are you waiting for. Get inside."
"Doctor." Clara said. "I'm tired. I've just had a wonderful night with Danny."
"Getting the Eye is more important than your boyfriend." The Doctor said. "Besides. New New York is special. It's one of the worlds where magic is possible. That means you can use your powers there."
Clara rarely went to a world where magic was possible. The only places she'd been where she could use her powers were the Enchanted Forest, Agrabah, Wonderland, Neverland, Arendelle, and Oz. She did want the opportunity to use magic again.
"You hate magic though." Clara said.
"I'm looking for magic." The Doctor said. "You could use magic to help me find it. Please just get in. The longer we stay here, the longer this will take."
Clara knew it was no use arguing with him on this one. So, wearing a red dress and black heals, Clara boarded the TARDIS for another adventure.
New New York, New Earth
The TARDIS materialized in a field across the harbor from the city. The Doctor and Clara stepped outside and saw a beautiful city in the distance. There were skyscrapers taller than any on modern day Earth and flying cars zoomed across the sky.
"It's amazing." Clara said.
"It's huge." The Doctor said. "Thats why I need your magic to help find it."
Clara took the Doctor's hint and extended her arms. She was preparing to cast some kind of location spell. However, something strange distracted her. There were cars flying through the air, but there was something else in the sky above. It was more unusual than anything else. In the distance, Clara and the Doctor saw an old pirate ship flying in the air. The main sail on this ship was not white. It was black. A pirate ship with a black sail was flying through the air, and coming towards the Doctor and Clara. The ship flew lower and lower. It was clearly trying to land in the harbor. The two time travelers instinctively ran closer to the water to see what this ship was doing here. The ship made a large splash as it hit the water and sailed closer to the shore. As it moved closer now in the water, the Doctor and Clara realized that they recognized this ship. It was the Jolly Roger, Captain Hook's ship. The Doctor and Clara soon recognized some of the people on the ship as well. They could make out the faces of Hook, Emma Swan, Regina, Henry, Mary Margaret, David, Mr. Gold, Neal, and Tinker Bell. There were some other people that they didn't recognize as well. The ship soon reached the shore and parked there. Upon seeing the Doctor and Clara, the Storybrooke heroes used magic to transport themselves to the ground.
"What are you all doing here?" The Doctor asked. "How did you even get here?"
"That depends on where here is." Emma said. "What is this place?"
"You didn't mean to come here?" Clara asked.
"We meant to go back to Storybrooke." Regina said.
"Back to Storybrooke?" The Doctor asked. "Where were you all before?"
"Neverland." Hook said. "Pan kidnapped Henry. He's the one with the heart of the truest believer. We got him back and left Pan there to die."
"Regina trapped Pan's Shadow on the sail to take us home." Mary Margaret said.
"So where did it take us instead?" David asked.
"You're on another world." The Doctor said.
"In the future." Clara added.
"How could we have time traveled?" Neal asked.
"Perhaps Pan's Shadow is more powerful than we thought." Gold said.
"You're five billion years in the future." The Doctor said.
"How many?" Emma asked, sounding very surprised.
"Five billion." Clara said. "We're here looking for the Eye of Birth."
"It's here?" Regina asked. "On another planet five billion years in the future?"
"It's in that city across the harbor." The Doctor said. "Somewhere."
"I was about to use magic to find it." Clara said.
"Let me." Regina said. "Let someone who actually knows what they're doing find it. Then we can use its power to send the ship back in time."
"Why don't we just take the TARDIS?" Neal asked.
"I can take all the people, but I can't fit the Jolly Roger through the TARDIS doors." The Doctor said. "We'll need the Eye if you want your ship to go back to Storybrooke with you."
Clara went over to the Doctor and whispered in his ear.
"Why don't you just use the Eye that's in the TARDIS to do that?" She asked.
"Because, if I just send them home now, they won't help us find the Eye." The Doctor said.
"So how do we find the Eye?" Hook asked.
"I'll find it." Regina said. "Somewhere in that huge city, I'll find it."