A/N: So I rushed to get this out before Turn, Turn, Turn aired, so there could be some spelling mistakes, obviously spoilers for Captain America: The Winter Soldier & The End of the Beginning. I hope you like it!

A War In Secret

Chapter 1: Cold Case

The Bus,

50,000 Miles above Istanbul, Turkey

2 Days after the death of Thomas Nash,

2 Days after the disbanding of S.H.I.E.L.D.

Coulson sat down in the remains of his office, 'this is worse than after the 084,' Coulson thought to himself, "We have nothing left, no weapons, no rations, no hope," Coulson said to the cracked desk.

"We have each other," Skye said in the doorway, Coulson had not seen her standing there, "We didn't have that two days ago."

The Bus,

50,000 Miles above Arlington, Virginia

90 Minutes after the death of Thomas Nash

30 Minutes before the disbanding of S.H.I.E.L.D.

"Put down the gun May!" Coulson shouted at the woman he had once believed to be friend.

"Drop it, Agent May," Skye came in from the cabin also pointing a gun at the pilot's head.

"Coulson, I can explain!" Melinda pleaded, "You have to trust me."

"No, I don't," Phil said, obviously shaken, "Now tell me the truth! Who are you talking to? The Clairvoyant?"

"NO!" May shouted, "It…"

"Spit it out, May," Skye said.

"It was a direct line to Director Fury," May said, "He wanted to know if you could figure out what that thing was."

"What the blue alien was," Coulson started lowering his gun, and Skye followed suit, "Fury doesn't know."

"No, it was gift from you know who," May said nodding at Coulson, "It was the mission he was on when he died. He thinks it was about the cargo, luckily he got the package back to the Triskelion."

"Who is you know who?" Skye asked, "Is some other super-secret S.H.I.E.L.D. legend that everybody but me knows?"

"His name was Quentin Cole," Coulson said, "May take control of the plane, get us to Istanbul as fast as you can."

"What about Ward?" Skye asked, "Do you still think he's a traitor?"

"And Jemma!" Fitz yelled from the lab, "She's still at the Hub! She could be in danger!"

"I have a favor I can use, I'll use it there," Coulson answered, "Don't worry, Fitz she'll be fine. And I need to talk to Ward."

"Boss," Fitz said staring at one of the lab computers, "We have a serious problem."

"What is it?" Skye asked cautiously, it was hard to believe that anything worse could come.

"Every S.H.I.E.L.D. secret ever was just put on line," Fitz screamed in his distinct scottish accent, "And… Oh my god."

"What is it?" Skye elbowed her way into lab, "Is it about me?"

"No, Hydra," Fitz said staring up at her, "Hydra has been growing inside S.H.I.E.L.D. since the beginning, Hydra was the Clairvoyant, alright I have a list of Hydra agents in S.H.I.E.L.D., and… Ward is not on it. Coulson, Ward's not with Hydra, he's clean!"

"And… Coulson left," Skye said matter of factly, "I don't think he heard you, Fitz figure out if anyone else on the team is on that list. I'll find Coulson."

"Yes, leave me to sort through 70 years of information," Fitz mumbled under his breath.

"Coulson, COULSON!" Skye's footsteps were heard throughout the plain, "I need to talk to you!"

"WHAT AREN'T YOU TELLING ME!" Coulson was pointing a gun at Ward, threatening to shoot him, "WHO ARE YOU WORKING FOR!?"

"I'm not working for anyone!" Ward pleaded, "I'm not trying to betray you! I'm working with you, and May and Skye, I'm working for S.H.I.E.L.D.!"

"He's telling the truth Coulson," Skye ran in, "Are you pointing a gun at him?" She was wide-eyed, "He's not working for the Clairvoyant."

"What do you mean?" Coulson turned towards her, still pointing the gun at Ward, "How do you know?"

"Hydra has been growing inside S.H.I.E.L.D. since it's founding," Skye explained, "And all of S.H.I.E.L.D.'s files secure or otherwise have just been published online. Including a list of all Hydra agents inside S.H.I.E.L.D. and Ward is not on that list, neither is May or Fitz, or even you. The whole team is clean."

"We should report to the Triskelion immediately," Coulson said, "Fury will want us to report."

"That may be a problem," Skye pulled out her phone and pulled up a video of a heli-carrier crashing into the Triskelion, "S.H.I.E.L.D.'s been shut down, we're done."

The Bus,

45,000 Miles above Istanbul, Turkey,

2 Days after the death of Thomas Nash,

2 Days after the disbanding of S.H.I.E.L.D.

"We have each other," Skye said, "We didn't have that two days ago."

"No, we didn't," Coulson said, "My top priority is finding out what that alien was, and who you're parents are. We may no longer be agents of S.H.I.E.L.D., but we're still a family, and we help our own. We will find answers Skye I promise."

"I'd recommend strapping in," May's voice rang out through the plane, "We'll be landing in Istanbul in about 5 minutes.

"I'll apologize to him, I promise," Skye said, thinking of the man that she had wronged.

5 Minutes later they had landed and surrounded the table in the center of the plane's cabin.

"Here are the details of the case," Coulson said, having Skye pull them up on the board, "Quentin Cole was the Deputy Director of S.H.I.E.L.D. before Maria Hill, he was killed in action smuggling a package back from a terrorist base, we now know the package was the blue alien in T.A.H.I.T.I., as Skye didn't find any of S.H.I.E.L.D.'s files on him, we believe Cole stored them on a remote drive outside of S.H.I.E.L.D. We believe Hydra killed him because they wanted the information, we also believe that they never found it."

"So we're looking for information that the world's greatest spy organization never found," Fitz said looking at his partner, "So we'll definitely find it."

"We do have one lead," Coulson said, "There is a man we believe has the file, and possibly Skye's parentage. But S.H.I.E.L.D. was never able to identify him, he goes by an alias and we believe he had Cole killed. He goes by the Broker."

"So now we're looking for two things the world's greatest spy agency never found," Simmons said, "I think Fitz was right, we don't really have a chance."

"We have something they didn't," Ward spoke up, "Trust, we trust each other, the last two days have proven this. We're going to find this bastard, and we will find you're parents Skye."

NEXT: ABDUCTION

A/N: Ok thanks for reading I hope you liked it, not a lot happened this chapter, but so much will happen in pretty much every other chapter. This will be a pretty long story, it's essentially a counterpart to my Arrow story, and chapter ten of that story will be posted in the next few days. So, as always, happy reading!