Just to clarify before anybody gets confused, the dynamic between Maleficent and Malekith in the Acolytes of Chaos storyline is going to be a lot like Darth Maul and Pre Vizsla in Star Wars: The Clone Wars season 5 or Long Feng and Azula in Avatar: The Last Airbender season 2. They each have their own agenda and both plan on disposing of the other once they get what they want. As for who's the Long Feng and who's the Azula or Maul/Vizsla in the partnership, that's up for debate until the story gets that far.

And head's up, this chapter's going to be a pretty long one. Naturally, the chapter titles are all going to be Hydra themed. And this is the chapter where the T-rating for language really starts popping up. A lot of the dialogue in the second half of the chapter is quoted from the Agents of S.H.I.E.L.D. episode "One Door Closes."

Episode 14: Cut Off One Head:

Avengers Tower – April 4, 2014

5 Months before Re:Coded

"How are we doing?" Natasha Romanov asked Maria Hill, newly minted Director of S.H.I.E.L.D. as the brunette woman typed furiously on the holographic keyboard in the common room of Avengers Tower. With the revelation of Hydra's infiltration of S.H.I.E.L.D., the agency was crippled and world leaders were looking for answers. While Hill, as Director Fury's lieutenant, assumed command of the loyal S.H.I.E.L.D. agents who remained and lead them in expunging the Hydra infiltrators. The S.A.C.K. members within S.H.I.E.L.D. had been preparing for this scenario for decades now, so the agency itself wasn't going anywhere anytime soon.

Unfortunately, things were complicated right now, and world governments wanted a simple answer. Which was why Agent Romanov would be testifying in hearings before congress and the U.N. all week defending S.H.I.E.L.D.'s good name and serving as a public defender of the agents who remained loyal to the organization and what it stands for. The new director herself would be spending that time assessing who was still loyal to S.H.I.E.L.D. and taking stock of their remaining base.

It had been a long day for all of them. Captain America was in the hospital after his fall into the Potomac, and Sam Wilson was busy keeping him company. Nick Fury had gone into hiding, feeling that it was time for him to step down from his position as director and let the world continue to believe that he was dead. Agent Barton was at his family homestead. And Bucky Barnes, until-recently-deceased Howling Commando and the infamous Winter Soldier, had managed to break free of his Hydra brainwashing. His memories were still coming back to him in bits and pieces, but he would recover fully in time. To prove he was on their side, he provided Hill and Romanov with what little intel he possessed on Hydra's locations.

But once Steve woke up, he was heading out again. He'd argued that they had a diminishing window of opportunity. Nobody in Hydra knew that he had broken free of his conditioning, so he could use that status to act as a Trojan horse, infiltrating the remaining Hydra bases in order to bring them down from the inside. Steve was hesitant to agree to that plan, not wanting to lose his best friend after he just got him back, but Bucky insisted that it would his way to atone for the things he'd done.

"Besides," he argued. "Once the U.N. puts me on trial for everything I've done, the secret will be out. We have to act now before that news reaches Hydra." Reluctantly, Steve acquiesced, and Bucky headed out to Eastern Europe two days after the battle, his memories of his past becoming clearer and more complete with each passing day. With Hydra exposed, the Avengers assembled within days of the battle to push the offensive. Hydra may have suffered a setback with Captain America's thwarting of Project Insight, but the ancient organization was far from beaten.

The Iliad – April 4, 2014

5 Months before Re:Coded

Gunfire rang out through the corridors of the Iliad as Barbara "Bobbi" Morse, Alphonso "Mack" Mackenzie, Isabelle Hartley, and two S.H.I.E.L.D. trainees made their way to the ships conference room. In the wake of Nick Fury's death and Hydra's exposure, Commander Hill had dispatched Morse and Hartley to one of S.H.I.E.L.D.'s aircraft carriers to confirm the fate of its commander, Agent Robert Gonzales, and either retake the ship from Hydra if at all possible, or exfiltrate the remaining S.H.I.E.L.D. loyalists and sink the ship if not. The Iliad's primary cargo was too dangerous to allow it to fall into Hydra's hands.

Eventually, they reached the conference room, and Bobbi nodded before pulled the door open as the five armed S.H.I.E.L.D. agents moved into the room, weapons drawn in case there were any Hydra operatives hiding in the room. Their expressions remained stoic as they made their way past countless dead bodies. But whether they were S.H.I.E.L.D. or Hydra was anyone's guess. As they crept through the empty room, Bobbi and Isabelle saw someone readying a machine gun from behind a table. Though they hadn't met the man, they'd seen his photo enough to recognize him without needing to see his face.

"Commander Gonzales, wait!" Agent Morse called out as she held up her hands to show she meant no harm.

"We're not Hydra," Hartley reassured the wounded officer.

"I've heard that before," the aged commander retorted angrily.

"I'm Agent Bobby Morse," Bobbi replied. "We're here under Fury and Hill's orders. Protocol AST-A06."

"Thank God," Commander Gonzales groaned as he lowered his weapon. "It's been a bastard of a day."

"Sir," Bobbi said. "Our mission is to get you off this ship and either retake it or sink it depending on whether we can gain control soon enough."

"That man there had an ax," the injured officer commented, gesturing towards the nearby corpse of what was presumably a Hydra agent. "Now I have it," he added before nodding towards the bloody gash on his leg. "Still left quite a mark." Explosions echoed through the halls of the ship as Bobbi the two trainees quickly worked to straighten Gonzales' leg while Mack told the man a story about how the most dangerous kind of pain was the kind you couldn't feel to take his mind off his leg wound as they worked.

"Hey guys," Hartley called out, rushing into the room from her position as sentry. "We gotta move. Hydra's closing in on both sides."

"His leg's bad," Bobbi explained as Mack and the trainees continued to bandage and splint Gonzales' leg. "Do you think you can clear a path to the top deck and ready the chopper?"

"An opportunity to kill more of these bastards?" Isabelle asked rhetorically, cheerfully chocking her gun as she spoke.

"I love your whole thing, you know that?" Mockingbird replied. "Hold out for them as long as you can. They'll be right behind you." Agent Hartley didn't even have to ask where her partner was going to go. Their orders were to retake or sink the ship once Gonzalles was rescued, so Bobbi was going to stay behind and rally the remaining S.H.I.E.L.D. loyalists while the rest of the group got the commander to safety. If there weren't enough loyal agents left to retake the ship, she was going to head back to the server core where they'd rescued Mack and the trainees and plant a disc that would remotely detonate every combustible weapon on board and sink the carrier.

"If I don't make it out," she went on. "Could you give this to Hunter?" She handed Isabelle a keychain for "Franny's Saloon," that was a memento of the times she'd shared with her ex-husband. Despite their frequent arguments and eventual divorce, she still cared about him.

"Bobbi, He's gonna be pissed," Izzy replied as she accepted the keychain. "You know that?" Agent Morse nodded in response before her combat partner left the room. As Mack walked up with a shotgun in his hands, she asked if he and the trainees could carry Gonzales up to the chopper before explaining her own orders. Mack wanted to stay and fight and protested that if she had to sink the ship there'd be no time for her to make it out before the Iliad was 80 feet underwater. Bobbi protested that the disc was designed so that she could remotely detonate it from a distance without risk of Hydra agents finding and removing it, but Mack nevertheless protested why Fury would send her on a suicide mission. Gonzales then explained about the ship's cargo and insisted on staying behind to help retake the ship.

"I can't let you waste your time or your resources trying to get me off this ship while it's in play," the commander said firmly. "I'm coming with you." Bobbi and Mack knew from his tone that he was staying to fight and refused to take no for an answer, and Mack continued to remind Bobbi that she didn't have to be stubborn and achieve her objective alone.

"God help us, I'm still the captain of this ship, Agent Morse," Gonzales said. "We're going to retake this ship together, no arguments. Now let's move." With that, the group made their way back out through the corridors until they met up with Agent Hartley. They found her fighting off Hydra goons with a knife, and once their foes had all been eliminated, she happily reported that a group of loyal S.H.I.E.L.D. agents had taken control of the top deck. Realizing that all Hydra agents left on the ship were now trapped on board, Gonzales ordered their ragtag group to fall back to the operations center.

Once they were all inside, the group armed themselves and set up a bottleneck inside the ship's command center. Despite being outnumbered three to one, the remaining Hydra agents were trapped. Now it was just a matter of luring them all towards strategically placed choke points to even the odds. By the end of the day, the Iliad was back under S.H.I.E.L.D.'s control. Although the agency was heavily crippled by Hydra's uprising, they would survive. With Maria Hill taking command of the remnants of S.H.I.E.L.D. and Hydra's forces on the run, those who stayed loyal S.H.I.E.L.D. would not vanish quietly into the shadows. They would stand and fight to protect the people of Earth.

So yeah, that happened. As I was planning the overall story of the Acolytes of Chaos saga, I realized that things would make more sense (and be a lot simpler) if S.H.I.E.L.D. didn't collapse at the end of Winter Soldier (since Agents of S.H.I.E.L.D. from the last third of Season 1 onwards is focused on rebuilding the agency, it was simpler to have it never collapse in the first place). And before anyone cries fowl about Cap's decision to disband it in the movies, there's a reason he didn't do it in this universe. But that reason is a spoiler for a later chapter.

And as for Bucky regaining his memories, I'm having it happen faster than in canon (since it's unclear in Winter Soldier and Ant-Man how quickly it's returning, I'm just going with the idea that it's happening slowly), because I wanted to have the Steve and Bucky thing happen earlier. As for Bucky going undercover to sabotage Hydra that was inspired by a number of different fanfics (like the Avengers/Harry Potter crossover Child of the Storm and the Percy Jackson/Avengers crossover And You Know Heroes Aren't Meant To Survive), particularly the latter one which had Bucky convince Quicksilver and Scarlet to change sides, which I'll be borrowing in order to have those two defect from Hydra without Ultron's existence, since Age of Ultron is does not happen in this universe (not entirely at least. It's like with Thor: The Dark World. Only part of that movie occurs in this universe. In the case of Age of Ultron, only that opening battle is canon in this universe. I did warn you all this would be AU after Winter Soldier)

Next chapter: we catch up with the rest of the Agents of S.H.I.E.L.D. cast in the aftermath of the battle at the Triskellion.