Prologue
Author's Note:: Welcome to my story. This whole premise is based off of something that Tony Stark said about Fury in Avengers: "His secrets have secrets." I don't know about you guys, but I was really curious about what that could mean, and the result of my curiosity was this story. Anyway, this chapter mainly serves as the background, so if you don't feel like reading cleverly written exposition, you can skip to the next chapter. Please, let me know what you think, and more importantly, enjoy!
Nick Fury's secrets have secrets.
For instance, there was the fact that directly after the whole Chitauri debacle, the World Security Council had ordered SHIELD to begin the E.P.I.C.S. Effort (Exploration of Projects to Impede Celestial Sabotage). EPICS was born out of the resistance to Phase 2, or perhaps more accurately, Thor's resistance to the project which was so strong he felt compelled to take their main source of power with him to another world. The goal of this new effort was to generate "better" (whatever that meant) deterrents and immediate response strategies to manage alien attacks, with many of the "innovative ideas" coming from the ashes of old projects that had burned out for various reasons.
From this secret arose another: SHIELD was putting the majority of their hope (and time and capital) into the resurrection of Project P.I.E.C.E.S. PIECES or the Pursuit of Intelligence Essential to Critical Extraterrestrial Situations was a project centered around developing the ultimate deterrent christened the Perditrix. The initial attempt to develop the Perditrix had ended after the World Security Council decided the deterrent had "unnecessary force for any conflicts in the foreseeable future" and therefore was a "misallocation of resources." Fury had had an issue with the word "foreseeable," but had been directed to let the project die, and it being early enough in his career for him to still feel obliged to follow orders, he did as he was told. Nineteen years later, now that they needed to revive PIECES, the creator and lead scientist on the project, Dr. Kendrick, was dead. It had been an "unforeseeable tragedy." Go figure.
Luckily, SHIELD still had possession of the journal Dr. Kendrick kept his notes in while originally working on the project. Unluckily, the notes were incomplete, and it was soon discovered that around half of the formulas Dr. Kendrick had written were not formulas at all, but names. It was unclear if the names were theories or researchers (as some names seemed to be coded and others were directly mentioned) or just random people, and it was also uncertain as to whether or not they were first or last names, as a few seemed to be very clearly first names, a few appeared to be very clearly last names, and a whole mess of names could be either. SHIELD was currently in the process of decoding all of these formulas and searching out various leads, the identities of these names becoming more secrets for Nick Fury to carry.
In fact, Project PIECES was surrounded by secrets, with another one being that about a month ago when SHIELD had started to really make headway on the project, an alien had been caught scouting out the facility where the majority of the work on PIECES was being done. It became very clear after a few interrogation sessions that somehow in the few short months that SHIELD had been working on PIECES, word had reached space about the device, and he had been sent to acquire the Perditrix. So, there was now an extraterrestrial threat on Project PIECES. Again, it had been unforeseeable.
However, the most pressing secret on Nick Fury's mind was one that had reached him a little less than half an hour ago. One of his secrets was now somewhat defunct. The alien was gone; he had somehow freed himself, knocked out a couple of Fury's top agents and the lead scientist on the case, stolen half of Kendrick's notes and then, while surrounded by agents, vanished into thin air.
It was with these secrets in mind that Nick Fury landed at the secret base near Cima, California.