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And so the world was saved. New York could start building again, Thor went with Loki to Asgard, Steve went to familiarize himself with the places that he knew from before the ice, Natasha had SHIELD breathing down her neck to get back to work and Clint said that he needed to spend some time far away from New York. As for Bruce, Tony invited him to spend some time at the tower that after a lot of cajoling had been accepted.
One day Bruce and Tony were in their shared lab trying to test different textiles for strechability. Hulk resistant pants were something that was sorely needed after the last battle. There were whole facebook groups of angry parents after the last battle were Bruce's jeans had not survived the transformation.
"Bruce I think the 4-way streching Lycra is still the best option."
"It doesn't breathe properly." Bruce sighed.
"Do you want to keep flashing Hulks bits? Because I have a new post from Karen that I can read to you about how she's sure she can take it and a post from Susan about how her kid is never going to get any Hulk toys ever."
"I would have to wear them all the time. I don't have time to change into them when it is an emergency. I cut you a deal if you wear lycra underpants for a week and still think it's the best solution I will give it a try."
"Ok. Let's look further then. Let's find a polymer that breathes and stretches. JARVIS give me a list of all fabrics with these properties."
"That fabric does not exist yet Sir. Now I have your attention, I have found something in the SHIELD files."
"Ok, hit me with it JARVIS."
"There seems to be a group operating within SHIELD. A group of which Director Fury is not part of."
"Wait, what SHIELD files?" Bruce asked
"Oh all of them. Did you thing I only looked up phase 2 when we were on the helicarrier? I copied as much as JARVIS could. Which is pretty much everything" Tony answers. "What makes you say that JARVIS?"
"There is a second level of encryption on a number of files which only a certain number of agents seem to know about but Hill and Fury have never looked at them or for them for that matter. Agents Romanova and Barton also seem unaware of them."
"Have you broken the encryption yet JARVIS?"
"I'm working on it Sir. It seems like it's designed to work with 2 keys one to make the information seem unassuming and one that gives the real information."
"Let me know when you are done with that JARVIS. So Bruce I believe it is time for a break, let's go upstairs and grab some food."
After the break Tony and Bruce decided to go work on their own projects for a while to let the stretchy pants problem rest and tomorrow they would take another look at it. People believed that Tony was the sort of genius that forgot to eat and rest when he was working and when he was in a difficult place mentally this was true. In those moments he would use his work to distract himself from the nightmares and invasive thoughts. He knew intimately how important it was to take care of yourself, the brain needed to be fed to keep functioning at it's best.
Tony had not completely been honest when he said he needed a break from the stretchy pants problem. He wanted to look at the files JARVIS had unencrypted and Bruce would be uncomfortable with that. Still believing that if he put one toe out of line SHIELD would use the 'room' where Loki was held in for it's original purpose. He walked into his workshop and sat himself at his workbench.
"JARVIS how far are you with those files?"
"I cracked the encryption during your break Sir. I did not want to disturb you and dr. Banner and I believed that you would want to take a look at this yourself first."
"Show me"
The holographic screen before Tony lit up and a skull with 6 tentacles appeared on the screen. Tony cursed and began scrolling through all the information.
"JARVIS do you have a cliffs note version of this?"
"Certainly Sir. Apparently SHIELD's founders Howard Stark, Peggy Carter, and Chester Phillips
recruited Arnim Zola, a hydra scientist, was recruited by SHIELD following the end of WWII as part of Operation: Paperclip. While working for SHIELD, Zola was also working to rebuild Hydra from inside the agency. At this moment there are several high ranking members of SHIELD with at least ties to Hydra, if not Hydra agents themselves. There are also mentions of an asset which if I cross-reference the dates coincide with a ghost assassins named the winter soldier. One of the only dates that does not coincide is 16th of December 1991. There are also certain parts of a SHIELD project, project insight, that are only for Hydra members."
Tony was flabbergasted his dad founded SHIELD and invited the enemy into his home. He thought his dad was smarted than that. Howard probably thought that he would be able to convert Zola completely or keep a good eye on him. This was too big to handle himself and he did not want to alert anyone at SHIELD which meant that contacting Fury, Hill or the assassin twins was impossible at this moment.
"JARVIS start compiling a list of all possible Hydra agents. Even the smallest tie I need to see. Screen Stark industries for SHIELD spies and make sure that they are removed from the premises. Give me a list of locations that only those with ties to Hydra visit. Thank you for bringing this to me JARVIS."
"Always a pleasure, Sir"
Tony grabbed his phone and called Steve.
"Hey, how soon can you be in New York I have something I need you to see."