I do not own the characters. DC and Marvel do.
This is set just at and after the end of the Institute Saga III and while other characters may appear, it is primarily about SHIELD.
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Chapter One
Crucible
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Nick Fury looked out of the panoramic bridge window at the debris-covered landscape slowly scrolling by below them. As they passed over the first of the wrecked helicarriers, he sighed.
"At least we'll have plenty of spare parts."
"It looks like, with a slight adjustment, we'll be able to replace the gravetic turbines with the repulsor-engine wings." Tony Stark noted and Fury nodded.
"Given the damage, I doubt that even one of those ships could be salvaged without requiring a total rebuild. What the hell were the Council thinking, anyway?"
"I think that we need to get them scanned to check that they aren't linked to Hydra." Tony said. "I've already made an appointment with Sage to check myself, Pepper and the rest of the Avengers. I don't think any of us are at risk, but…"
Fury snorted. "You're setting a good example? You?"
Tony paled. "Aw hell! I'm becoming… respectable! No! I'm too handsome to be respectable!"
Fury smirked at the panicking multi-billionaire, then turned his attention to the orbiting screens showing different views of the three battlefields.
"Sir!" A voice called, "Communication from Governor-General Zod, Apocalypse has been secured in stasis."
"Communication from Genosha!" Another voice called. "King Marko sends his regards and… thanks us for his new Kryptonian Guardian?"
"The clone." Fury and Tony chorused, then they glanced at each other.
"The clone that Magneto had made. Has to be her." Tony continued and Fury nodded.
"So, Genosha is about to get its own Kryptonian." Fury grumbled. "Who next?"
"Well, Doom has two, sorta." Tony shrugged as his fingers danced across a nearby screen. "Pulling up battlefield after-mission stats. The air force took significant losses, almost half the craft were shot down by the Sentinels although all but seventeen pilots managed to eject. No hero fatalities, but several of the teams will be at half-strength or below as their members heal. The military ground forces report only a few injuries, but they hadn't fully mobilised by the time that the action was finished. They're moving in now to help with the clear-up."
"It's going to take months to get things cleared up." Fury sighed, then he summoned a new screen. "And the Triskellion… sorting that mess out will take years."
Tony blinked. "What? But… it was barely damaged!"
"But Hydra were inside from the first day." Fury countered. "They infiltrated SHIELD before we even started building the damned place! Who knows how many hidden rooms and spy systems are in it now! And as for the staff… I'm going to have to hire a team of telepaths to sort out the SHIELD agents from the Hydra infiltrators."
"Shit." Tony agreed in realisation. "Man, am I glad that I'm not in line to lead SHIELD."
"Number four, actually." Fury said absently and Tony froze.
"What?!"
"You are the fourth leader of SHIELD." Fury repeated. "I'm number one. Should I fall, Abigail Brand is second, then Jasper Sitwell. You're number four due to your patriotism and experience in leading large organisations."
"What about Cap?" Tony protested. "He's…"
"Too patriotic and still catching up with modern technology, although the new stuff from New Krypton isn't helping him much." Fury sighed. "He's number fifteen. Just before Reed Richards."
"Reed is number sixteen?" Tony asked in disbelief.
"Eighteen, actually." Fury corrected as he turned back to look over the battlefield once more.
"Sir."
"Coulson." Fury nodded. "I have a mission for you."
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Agent Phil Coulson stepped onto the bridge of the Helicarrier, his gaze briefly darting to the smoking wreckage on the ground below.
The Bridge crew were far more somber than normal, the atmosphere of the Bridge heavy, but somehow still triumphant. To one side, Tony Stark stood in his Iron Man armour, his face a rather amusing mix of emotions as if he had received some news that he was uncertain how he should feel about.
"Sir."
"Coulson." Fury said without turning round. "I have a mission for you. I need you to visit Governor-General Zod. It seems that we need a new Triskelion."
Coulson blinked, his mind darting through the chain of logic. The facts assembled in his mindscape and he mentally nodded as he put the disparate pieces of information together.
"Understood, sir. I agree that there is virtually no chance that Hydra could have infiltrated New Krypton."
"You certain that he isn't a telepath?" Tony asked and a corner of Coulson's mouth briefly twitched upwards before he got himself under control again.
"Limits, sir?"
"Try not to bankrupt us." Fury shrugged. "Otherwise, use your best judgement."
"Of course, sir." Coulson nodded. "May I suggest we use one of the alternate sites to locate the Triskelion II?"
Fury looked blank for a moment. "Explain."
"It would be cheaper given how reinforced the Triskelion is and thus how difficult it will be to demolish and clear. In addition, once we have removed all of the classified technology, the building could be re-purposed. It would take only a relatively small effort to turn it into a shopping mall and apartment complex. We could even maintain a few safe-houses in it, no-one would expect that."
"An excellent idea." Fury finally agreed. "It would also provide a welcome boost to our funds."
Phil nodded, then turned and walked off the Bridge. Making his way through the corridors, he paused outside a reinforced room just long enough to present his security pass, then he entered it, pausing briefly as he looked at the Door.
The portal was set into a three-meter-square slab of Kryptonian metallic-crystal alloy which encased all of the inner workings, protecting them from damage. A raised walkway led through the Portal, a walkway that was set above a large bundle of pipes, cables and conduits which acted to link the Helicarrier to the other Door-enabled SHIELD bases, although the Triskelion link was now non-functional due to the Apocalypse incident.
Resuming his progress, Coulson stepped through the Door and onto the opaque-force-field protected SHIELD balcony in the Hall of Doors. Once again, he had to pause for the door to open, then he stepped out onto the walkway, turning right as he headed for the Door that linked to the newer Hall of Doors on New Krypton, nodding politely to the people using the Hall as he did so.
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"…and how was this even allowed to happen?" One of the faceless silhouettes on the meeting room screens demanded.
"It happened because of all the threats that SHIELD has prepared for, the return of a three-thousand-year-old omega-class mutant tyrant was not one that was foreseeable." Fury half-snarled. "Rest assured that once the planning division are cleared, they will be asked to put together plans for other myth-based eventualities, including an attack by Galactus if necessary."
"Who?"
"Galactus. According to the Kryptonians, it's an ancient planet-devourering entity." Fury shot back. "Apparently, although it destroys planets, its very presence prevents something worse from entering our universe, so destroying it isn't a viable option."
"Surely if you can destroy it, then whatever comes after it can be destroyed as well?" One of the other figures asked and Fury shook his head.
"Unlikely. I've spoken to Odin about this and Galactus is supposed to act as the lock, its very existence holding back a being so powerful that it took the Asgardians, the Celestials, the Eternals and the Kal'tash to lock it away. Almost three-quarters of each race died in the process with the Kal'tash being wiped completely out of existence. Do you honestly believe that we are powerful enough to match them?"
None of the figures replied and Fury nodded in aggrieved satisfaction.
"Good. Moving on. Now that we know that SHIELD is compromised, I've already started to reconfigure it, Only those who pass a telepathic scan by a trusted telepath or who pass other tests that I am arranging will be allowed to serve in the new SHIELD. I had Xavier check me to ensure that I wasn't a Manchurian Candidate. I passed."
"If SHIELD is compromised, what about the others?" A female silhouette asked and Fury bowed his head slightly.
"We have no choice but to assume that all departments have been compromised to some degree. SWORD is currently performing its own screening, having secured the services of a couple of telepaths from the Justice League. We have also placed an order with Black Ink for their truth-potion, Veritaserum, with the application and questioning to be overseen by their own people. Since neither organisation is native to our reality, they will not have been infiltrated. We are also preparing to start negotiations with the Yamanaka clan for the use of some of their mind-walkers."
"How long will it take to verify and re-assign your people?"
"Hard to say." Fury replied. "Best case scenario, maybe six months, assuming that the veritaserum works as expected. Worst case? Several years with no guarantee of success."
The figures on the screens moved as if they were talking to each other, then one of them spoke.
"You have our full support, Director. It is good to know that you are in control of the situation. We will not keep you from your duties any longer."
The screens blinked off and Fury glared at them.
"Control, hell." He muttured as he turned to leave. "If I had control, this situation wouldn't remind me so much of the snakes on a m*****f***ing plane. And that was a truly f***ed up undercover mission."
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The screens in the study lit up and the woman in the chair looked at the silhouettes on the monitors before her.
"Alright." She said in a commanding voice. "Does anyone have any idea of what the hell this Yamanaka clan is and where they are?"
"I think I might." One of the figures finally said hesitantly. "I think they were mentioned as part of the report on the inter-reality diplomatic missions, but I'm not certain."
"That gives us a place to start." The woman nodded. "I shall begin checking the reports to get more details. We shall re-convene tomorrow at noon."
The screens went blank and the woman tapped at her computer, setting up a search through the records available to her. A couple of moments later, her eyebrows shot up.
"Ninja?"
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"Agent Coulson?"
Phil looked around, then his gaze rose as the owner of the voice that had hailed him lowered herself to the ground.
"I'm Sabra." She said with a slight smile. "United Krypton Intelligence Service."
"I thought that you were a Mossad agent." Phil remarked and Sabra nodded.
"I was, but Mossad was folded into the UKIS. Well, I say folded, but since there were only three Kryptonians in their Military Intelligence…"
Sabra broke off with a slight shrug. "Anyway, I am here to take you Lieutenant-Governor Faora. If you will come with me?"
Phil quickly took position by her side as they walked through the flows of people passing through the New Krypton Hall of Doors. Phil looked round curiously, then he almost halted as a centaur trotted past, a young girl perched on his back.
"Was… was that a New Olympian?"
"He was." Sabra confirmed. "They are starting to spread out more, interacting more with the other nations. Well, I say nations, it's more similar to the United Kingdom, really."
"So which one is Scotland?" Phil deadpanned, only to receive a flat look in reply. "Sorry."
"The metaphor doesn't really hold up all that well." Sabra admitted as they exited through a portal that led them out of the base of an obelisk. "The car is this way."
Phil felt his eyebrows raise as he saw the vehicle that they were heading towards. The car looked perfectly normal, at least until you spotted the lack of wheels, or indeed the wells for the missing wheels to fit into. Instead, the open-topped car rested on a set of retractable landing pads.
"Ground-effect anti-gravity technology." Sabra explained as she vaulted into the drivers seat, not bothering to open the door. As she began tapping various controls, powering up the vehicle, Phil opened the passenger door and sat down.
"Seatbelt?"
"Tractor field." Sabra said as Phil felt himself being pulled gently but firmly into the embrace of the seat. An instant later, the car rose slightly and Phil heard the whine of the landing gear retracting.
"Hold on." Sabra smirked, then Phil was almost slammed back into his seat as the car leapt forwards, banking into a turn before straightening out and speeding up.
"There's no breeze because of a low-powered forcefield." Sabra said, pre-empting his question. "You have questions, so now is the time to ask them."
"So that is why we didn't simply take a Door to our destination." Phil realised.
"That and you don't have a valid security pass for that particular Door, yes."
Phil nodded. "I see. Getting into the habit of security when enemies can't reach you, so that you are prepared for when they can. Very clever."
"I'm glad you think so." Sabra chuckled.
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Author's Afternote – Yes, Snakes On A Plane is now IS-canon!