Chapter 36: Director of the SHIELD
Bruce turned his attention toward his old body. The machines were still working and had already extracted 99% of the Infinity energy. As much as he wanted to destroy his body, it would be such a waste to let the precious energy go. He could use this energy for a lot of things, like making fake Infinity Stones or maybe he should give it to Morgan and help her master her power to manipulate that energy. So, he decided to store it for now.
After that, he destroyed his old body, copied all the data, took the solidified energy crystals, and activated the self-destruct. He couldn't let a cursed place like that exist any longer. By the time he came up to the surface, the underwater lab exploded, creating a massive water pillar like in an action movie. The sea swallowed the lab, so deep and strong that it would soon crush the last bit of evidence of Hydra's plan.
Bruce opened the map on his HUD and checked on Morgan. Natasha, Selina, and Harley were in his safe house with Morgan. Other than him and Natasha, no one knew the location of that place, and that place was surrounded by the most secure technology known to mankind. He flipped through the screens and saw his daughter sleeping soundly in the main room.
He sat down on the muddy ground of the island and looked at the endless sky and the never-ending ocean. So peaceful and so quiet, with no sounds to disturb it. He was so happy and eager to meet his family once again, but the truth and reality completely broke him. "Hahaha..." A dry laugh came from his throat as the tears poured from his eyes, and his heart shattered, as it felt like he was living a lie.
Then the wind blew through his hair, bringing the scent of the ocean, the taste of salt from the ocean, and the subtle warmth of the fading sun, which gradually disappeared below the horizon.
Some part of him had wanted the old times to return...
"Thank God," Bruce for the first time joined his palms and thanked God for keeping Morgan alive. "If something happened to her, I don't know what I would have done... But the truth... It fucking hurts so much. To think Pepper was Hydra's puppet and Fury was the leader of Hydra the whole time... Never saw that coming." He sighed and stood up.
He flew away, making his way to the safe base.
...
...
The news broke like a tidal wave across the world. The resurrection of Tony Stark, Iron Man, sent shockwaves through the media. Broadcasts, social media platforms, and news sites exploded with headlines:
"IRON MAN RETURNS FROM THE DEAD!"
"PEPPER POTTS EXPOSED: HYDRA'S INSIDE WOMAN?"
"NICK FURY: HYDRA LEADER ALL ALONG?"
There was chaos everywhere. Governments scrambled to make sense of the information. Intelligence agencies around the world initiated immediate internal investigations, fearing Hydra infiltration. The global trust in S.H.I.E.L.D. shattered overnight, and protests erupted in cities worldwide, demanding accountability.
While Morgan was still sleeping, Pepper was under arrest, Bruce decided to take this chance to eliminate the remnants of the Hydra from the face of the Earth. He sat on the chair beside Morgan's bed and activated his VR headset. The holographic screens appeared before the space around him, he focused on the most secure system he could hack into—Fury's private server. The server was disguised behind layers of false data, quantum encryption, and unique identifiers, but Bruce's skills had long since surpassed any cybersecurity measures SHIELD or HYDRA could deploy.
He worked methodically, slicing through firewalls and decrypting secret files, his eyes scanning thousands of lines of code, surveillance logs, and hidden communications. It was a network only Fury himself and a select few had access to. As he went through the data, he found a hidden sub-server, and on opening it, his eyes narrowed at what he saw.
The server was operated remotely, managed by a Skrull—posing as Fury's wife. His jaw clenched in anger as he pieced together her role, realizing she had been Fury's most trusted confidant and, unbeknownst to even the highest-ranking agents, the shadow director of his Hydra operations.
His fingers flew across the keyboard, hacking into her live feed. There she was, sitting in her room and reading a book, completely unaware of her fate. Bruce controlled the Sentinels outside her house to blow her up before she even had a chance to understand what was going on. Just like that multiple laser beams and missiles shot out and ripped that alien and burned down the house, killing the imposter instantly.
Bruce then turned his attention back to the server, scanning through the detailed files. He found a comprehensive list of HYDRA agents embedded within SHIELD, government organizations, and even other Avengers' personal networks. Fury had kept meticulous records, using this information to play both sides and maintain control over SHIELD's fractured loyalty.
He compiled all the damning data into a secure file and encrypted it with a one-time key. He opened a live feed to Natasha, Clint, and Jennifer, who were gathered in a SHIELD command room.
"Tony?" Natasha asked, noticing the hardened look on his face. "Wait! I should call you Bruce or Tony?"
Bruce smiled, "Call me Bruce. I got used to this name, I guess. But I think the world will address me as Tony. I should make an official announcement soon, I guess."
"Oh right." She smiled. "So, what's new? Did Morgan recover fully?"
"Mm. Yeah. She's sleeping." Bruce nodded with a smile. "She needs it... I will call you when she wakes up. But till then let's get rid of the traitors for good this time. I've got something for you. A list of every HYDRA agent embedded in SHIELD. Fury's been running this entire operation with his wife by the way. She's dead now. I just took care of her," He said bluntly.
"Wait! She was also involved?" Clint asked, rubbing his temple in pain.
"Yes," Bruce confirmed. "She was managing HYDRA's operations directly through Fury's private server. I've got the complete list. You three need to clean the house immediately. Use this data, find every traitor, and eliminate them. No hesitation."
Jennifer glanced at Natasha, then back at the screen. "You want us to kill them all? There's no going back from this."
"They made their choice when they decided to infiltrate and destroy our lives from the inside," Bruce's voice was icy, his eyes cold. "If we leave even one, it'll start all over again."
Natasha nodded, already formulating a plan. "We'll get it done."
Bruce uploaded the data to their system, and Natasha quickly began cross-referencing it with current SHIELD personnel. It was an extensive list, names of high-ranking officials, field agents, and even members of Fury's inner circle.
Clint cracked his knuckles. "Looks like we've got a lot of work to do."
Jennifer, now in charge of SHIELD's legal department, stepped forward. "I'll handle the legal side, declaring martial law within SHIELD for an immediate takeover. The rest of the organization will follow our lead once we start making arrests."
With Bruce's intel, Natasha, Clint, and Jennifer moved swiftly. Natasha and Clint personally led the strike teams, targeting HYDRA agents embedded deep within SHIELD's infrastructure. It was a ruthless operation, and they spared no one.
Within hours, chaos erupted throughout SHIELD's bases worldwide as agents were pulled from their posts, dragged into interrogation rooms, or outright executed if they resisted. Jennifer coordinated the legal dismantling of Fury's power structure, dissolving his secretive black ops divisions and reallocating resources to root out any remaining HYDRA cells.
Bruce monitored the progress from his safe house, watching as the traitors were either killed or captured. He saw their faces, many of whom he had once considered allies. Fury's betrayal ran deep, and it left a bitter taste in his mouth.
The operation lasted through the night, a relentless purge of HYDRA's influence. By dawn, the remnants of Fury's HYDRA network were shattered, and the agents were either eliminated or taken into custody. Natasha, Clint, and Jennifer regrouped at SHIELD HQ, looking over the list of those still unaccounted for.
Natasha took a deep breath, staring at the names crossed off. "It's done. We got most of them, but a few slipped away."
"Don't worry about the stragglers," Bruce said through the comms. "I've already deployed the Sentinels to hunt down the rest. They won't get far."
Clint leaned back in his chair, exhaustion evident on his face. "So, what now? We rebuild SHIELD from the ground up?"
"Exactly," Jennifer said, stepping forward. "With Fury gone, we need to make sure this never happens again. Full transparency, no more secrets like this."
Natasha nodded in agreement. "We're in control now. Let's do it right this time."
"Natasha, I know you spent years trying to save my daughter, even through the war. I don't want to ask any more of you than what you have done for the last ten years. But I want to burden you with another big responsibility... Become the new Director of the SHIELD," Bruce announced from the screen.
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