Disclaimer: I don't own Agents of S.H.I.E.L.D. I don't own any part of the extended Marvel Cinematic Universe. I'm honestly not sure who owns what when it comes to the complicated issues of copyright for various aspects of a comic books and comic-based media. Whoever it is that owns the copyrights to the various aspects of Agents of S.H.I.E.L.D. (Presumably Marvel, among other groups and People, including apparently Disney) and the extended MCU owns them. I don't.

Author's Note: I am not what one would call an expert on Marvel. Indeed, I haven't read a single Marvel comic – however, I have done some reading on the Marvel Universe, and I am pretty familiar with the extended MCU. If I get something about the MCU wrong, feel free to correct me in a review or message. If I get something about the Marvel Universe (i.e. material not from the MCU) wrong, feel free to point it out to me, but I reserve the right to ignore non-MCU material.

Thanks to Energy Being for beta-reading this chapter.

A Different Choice

By Alkeni

Chapter 1: The One Thing He Wanted

S.H.I.E.L.D. Jump Jet En Route to the Fridge

The Day That S.H.I.E.L.D. Fell

S.H.I.E.L.D. had fallen.

The Hub had been retaken, the Insight Carriers had been destroyed and Alexander Pierce was dead. But he'd taken S.H.I.E.L.D with him. Captain America and Agent Romanov had seen to that when they'd dumped all of S.H.I.E.L.D.'s files onto the internet. An organization built on secrets, compartmentalization of information and keeping information from the public simply couldn't survive a blow like that. Especially when they missed a secret as massive as Hydra infiltrating them for seventy years.

Of course...Ward had been expecting the fall of S.H.I.E.L.D. for...a long time. He hadn't expected to happen when it did, but he'd known it was coming. And when Nick Fury picked up on what was going on, Hydra decided to overplay its hand. And so, the other thing he'd been expecting hadn't happened. Because Hydra had failed.

Even if he hadn't known for a fact that Hydra was still out there, if he actually was the loyal S.H.I.E.L.D. agent he'd long pretended to be, Ward still wouldn't have been naive enough to think that Hydra's failed bid to 'come out of the shadows' and take over the entire world was the end of the organization's threat.

But Ward did know for a fact that Hydra wasn't dead. He knew that Hydra had assets outside of S.H.I.E.L.D. as well as inside them. It was still a going concern, and Ward knew the names of other leaders that would be stepping up to take over from Pierce and Sitwell and the rest who were dead or captured had been. Whitehall. Strucker. List. Those were the big names that Ward knew, even if he'd never met any of them. And there were others. The Hydra motto didn't come from nowhere. There were more heads ready to grow.

Hydra was still active.

And John, with his need for the dramatic, had decided to blow his cover when he hadn't needed to. Coulson had told him just how he'd realized John was the Clairvoyant. It was a deliberate move – John had made yet another of a line of questionable decisions.

Ward hadn't always found those decisions questionable – he'd only, in hindsight, begun to see them as questionable in the last half-year working with Coulson and his team on the Bus.

Like ordering Quinn to shoot Skye. Even now, Ward's blood boiled and he felt a pain as though he'd been shot, not her, at that thought, at the memory of Skye laying there, bleeding out...and John's smug, glib explanations...and what hurt Ward even more was how he'd just stood there and taken them.

He'd failed Skye then.

And he was going to again. He was going to have to. Which was why Garrett was showing no signs of worry, as if he knew he was going to get out of this. Because he knew Ward would save him.

Ward owed John. After all that John had done for him...he couldn't just let John rot in the Fridge. He couldn't just let him die...

Ward closed his eyes and the image of Skye's face floated unbidden to the front of his mind. Of Skye dying...dying because of what John Garrett had ordered...

Skye.

He hadn't wanted it. Hadn't expected it. But somehow, someway...Sky had gotten to him. Gotten him to care. She'd been...color. Color in an otherwise dull and gray existence.

Over the last fifteen years, Ward had found that there were only two types of people. Those that wanted to use him – for their own twisted amusement or simply for a mission. Almost everyone fell into that category. And then there was John. The man who had built him up, who had saved his life more than a dozen times ways in more than a dozen ways.

For the last fifteen years only one thing had mattered to Ward, above even his own survival, Paying John back... for the debt he owed, for saving him, for putting him back together. Giving him purpose. And when John's cybernetic implants had started failing, when every other option had been exhausted, Ward had done what he needed to do for John and taken the position on Coulson's team. He'd given Coulson a project, someone to fix, and then manipulated everyone around him into trusting him. All to find out how Coulson had survived, how he'd come back to life.

He'd taken it as just a mission – he'd done countless missions, for Hydra and for S.H.I.E.L.D. His loyalty had never been to either. Just to John. Only to John.

And then, suddenly, there had been Skye. Just some little hacker that Coulson had picked up, another stray on a plane full of them, who shouldn't have meant anything to him… but now, what he was ready to turn his back on the only man who'd ever really cared about him. For her. All for her.

In just a few minutes now, there was something he was going to have to do. And when he did it...when Skye found out that he had done it, that he had lied to her, lied to everyone...betrayed them...betrayed her...she'd never forgive him. He'd lose her completely, as much as part of him entertained the fantasy he could convince her. Somehow.

Hydra was everything Skye hated. Yes, she'd hacked S.H.I.E.L.D. fought against while a member of the Rising Tide. But though S.H.I.E.L.D. had been built upon a foundation of secrets, it's purpose was protection. To save lives, simply put. Skye had grown to understand that, respect that...

Hydra though...Hydra was built on lies and betrayal for the purpose of control. A group of murderers. Evil.

Skye...Skye was the one thing in his life he'd ever wanted for himself, the one thing that made him feel like he wasn't just a rotating series of masks. And now he was going to destroy any chance of having it – any chance of her returning his feelings for the man he owed everything to. And even...

Even if Ward could have brought himself to abandon John...a choice that tempted him...even though he knew he couldn't do it, John would punish him. He'd reveal everything Ward had done for him – for Hydra. And that would damn him in Skye's eyes just as much as if he sided with John. Never mind that Ward's loyalty hadn't been to Hydra...he'd still end up dead, or in the Fridge right alongside John. What he'd done wouldn't be forgiven by S.H.I.E.L.D. And he couldn't say he regretted what he'd done. Not really. Not even now.

The only thing that he regretted was the fact that it forced his hand. He had to free John Garrett, if only because that was the only thing that would give him just a little more time as the wonderfully… good S.H.I.E.L.D agent that Skye saw him as.

He had to break cover and betray the team. Betray Skye in such a way that he'd never be able to come back from it.

Agent Jacobson walked out of the cockpit and nodded to Agent Hand. "Course is locked ma'am."

The clock was ticking now.

"Good." Hand replied confidently. She looked at John Garrett, then to Ward. "He's not telling stories now, is he?" No. Something to be grateful for. One got tired of John Garrett's stories quickly. Ward was no exception. He said nothing, only half-listening to Hand talk, focusing on what he'd have to do soon. Hand turned her gaze back to John. "You know what I'm thinking, Agent Garrett?" Hand proceeded to answer her own question. "I'm thinking the Icebox of the Fridge is a little too comfortable for you." Where is this going? Ward didn't visibly react, but Hand's words were sending his mind racing. "Maybe we should put you a little deeper underground." John finally turned to look at Hand, but his expression didn't change. Hand turned back to him. "What do you think, Agent Ward? You shot the wrong Clairvoyant before. Care to shoot the right one?"

Ward knew it was exactly the opening he needed to take. The opening John would expect him to take. But...he could barely believe the suggestion was coming from Victoria Hand. Straightlaced, by-the-book Hand. Then again, she had ordered her men to shoot up the Bus, without any attempt to find proof that Coulson was Hydra – her entire case had been speculation and suspicion. She had a ruthless streak – but this...

He really hadn't expected this.

Ward didn't need to make a show of thinking it over...because he was. He knew that this was the kind of window of opportunity John was expecting him to take. But a part of him screamed in Skye's voice for him to kill John now. To get rid of the Damocles Sword over his head. If he killed John now...he wouldn't have to betray Skye...wouldn't have to throw the one thing he'd wanted for himself away.

He couldn't let John free...because then John would come for Skye. Skye had been given the G.H. 325 serum that John wanted. That John needed. Ward couldn't let that happen.

He didn't owe John that much, the part of him that wanted him to kill John. He didn't owe him Skye.

Ward stood up, drew his gun, switched off the safety and met John's eyes. He saw the expectant glint in them – for a moment, he wondered if the others noticed it, but no. He only saw it because he knew John as well as he did...

If Ward had been a different man, his hand might have shook as he raised the gun, pointing it at John, as if about to shoot him. He had to do his job. He had to save John. He had to help him survive. He had to repay him.

Ward stood there, the gun still aimed at John, but he didn't move. He didn't pull the trigger. Five seconds. Ten seconds. Fifteen seconds. Twenty seconds.

Apparently, twenty seconds was too long for both Agent Hand and John. But John spoke first.

"Come on son. We both know you're not going to pull that trigger. I know where your loyalties-" Before he could say anything else – before he could out him – Ward hit John across the face with the butt of his pistol.

I can't do this. I need more time.

Ward had always prided himself on his ability to make decisions – even 'hard' ones – quickly and effectively. He'd needed that skill working in the field as a specialist. But now he couldn't decide. He was torn between impossible choices, and it was John's fault. John had blown his own cover and forced Ward into this position.

"Agent Ward!" Hand was terse. "I suggested shooting the real Clairvoyant, not beating him. Either kill him or lower your weapon and sit back down."

"No." Ward replied, a decision forming in his mind as the image of Skye in that medical pod bleeding...dying came to the fore of his mind again. Ward wasn't going to fail Skye again...not...

Not completely. But, even now he couldn't kill John. He couldn't shoot him.

John started to smirk just as touch, thinking he knew what was coming, but his expression began to change has Ward continued to talk.

Ward's words came fast. He had to get them out now. Before it was too late. Before John said anything. Before he changed his mind.

"I agree he should die." Ward told Hand. "To pay for hurting," Skye, "all the people he's hurt. All the deaths. But a bullet is too easy. Too clean." Ward lowered his gun and holstered it. He owed John too much – but he refused to throw away Skye. Throw away any chance he might have of Skye ever returning his feelings. Feelings he hadn't meant to develop, but that he had.

"You're gonna do this. You're really gonna do this?" John sounded utterly unconvinced. "After all I've done for you, you're gonna -" John seemed to read Ward's thoughts on his face. "This is about that hacker? Really? Sure, she's a looker, kid, but come on!" He laughed, "She has to be really good in bed for you to-" Ward punched John in the stomach, twice and then pulled him close by the front of his shirt, kneeing the still handcuffed man in the gut. He murmured in John's ear, making sure the man grasped the picture of exactly what was happening.

"We both know that your Deathlok implants and the Centipede serum will let you survive a drop from this distance. Probably." They weren't, all things considered, actually that high up. A normal human wouldn't live through such a drop, but if anyone could, it was John Garrett. "All debts are paid – and this is more than you deserve." Before John could say anything else, Ward kneed him in the stomach again. If he had no breath, he couldn't talk.

"Agent Ward!" Agent Hand cut in, her hand going to his shoulder and pulling him off John, who, deprived of Ward to lean on, fell to the ground unceremoniously. "Beating a prisoner merely for the satisfaction it would give you is not acceptable. Or else I'd be right there with you. But we're still Agents of S.H.I.E.L.D. and that means there are things we don't do."

S.H.I.E.L.D. doesn't exist, Hand. Ward didn't roll her eyes. It wouldn't do for her, for anyone to realize just how little respect he had for S.H.I.E.L.D. They'd been too blind to see what was happening right in their midst.

S.H.I.E.L.D. was dead. Ward hadn't chosen S.H.I.E.L.D.'s side – in so far as it was even a side. He'd taken Skye's side, and he knew where Skye would want to stay.

"You say a bullet is too easy, and I'm inclined to agree with you." Hand agreed. "So what would you propose?"

"Throw him out of the plane. Let him splatter all over the ground." John started to laugh, but Ward ignored him, and the rest probably thought he was just nuts. "I think that would be about what he deserves."

Hand looked at him carefully, "Doesn't really fit with your record, Agent Ward. You've always shown a preference for clean, efficient kills." The Level 8 Agent didn't really seem suspicious so much as curious.

"Those kills were just the job." Whoever he was really working for. "But Garrett was my S.O. He betrayed me, he betrayed S.H.I.E.L.D. After everything he's done – after nearly killing my team more than once..." Ward paused a moment, and then, "after ordering Quinn to put two bullets in Skye...the last thing 'the Clairvoyant' deserves is a clean death." Which was entirely true. Even if Ward knew John would survive. And even if Ward didn't especially care about his former S.O. betrayal of S.H.I.E.L.D.

Hand nodded. "I thought it was something like that." She nodded to Agents Jacobson and Chaimson, who each grabbed one of John Garrett's arms. "Would you like the honors then?"

Ward nodded and approached the back of the plane, the other two agents dragging the still chuckling Garrett right behind him. Ward found the release for the entry ramp and switched it. It started to lower, and Ward grabbed onto something with one hand, holding on as the wind started to pick up. Chaimson and Jacobson took Garrett up to the edge, then stepped back, moving quickly and wordlessly back to their seats. This was up to Ward now. No one but him.

Ward stood in front of John, making sure that his S.O. couldn't step away from the edge.

"You think this settles all debts?" John barely managed to get it out over the sound of the wind whipping all around the two of them. "I own you, Grant." He laughed one more time. "See you on the other side, kid."

Silently, not trusting himself to say anything, Ward pushed the original Deathlok out of the plane, watching the man fall out of sight before stepping back and closing the plane. There was a chance he'd live. A chance he'd come back...a chance he'd try to hurt Skye again.

Ward could only hope he could bring himself to kill John next time they met. But one way or another, he wasn't going to let the man hurt Skye. Never.

Ward closed the ramp and walked back to his seat, sitting down without speaking.

Hand raised an eyebrow and looked at him, a wondering tone in her voice. "Garrett seemed fairly confident that you weren't going to kill him."

"He was my S.O. We went through a lot together. He saved my life – more than once." Ward told her entirely truthfully. "I guess he figured that meant I'd just ignore everything else he's done. He was wrong." He was only wrong because of Skye, though. If not for her...

Well, Ward would have stayed loyal. He owed John Garrett everything. But Skye was more important.

Command Center, The Fridge

The Day After S.H.I.E.L.D. Fell

They reached the Fridge without any significant incident, which was fortunate. Ward had spent the rest of the hours-long flight to the Fridge thinking about what exactly John would do next. Ward knew a lot about what John had planned, mid and long-term, but not everything. And projections would have changed, given that Hydra was out in the open.

Now, though, he was sitting in one of the chairs at the edge of the Command Center, absently watching Agent Hand and her people secure the Fridge against any coming attack. From Hydra, from the friends and allies of everyone else locked up in here, even from national governments. This was an illegal terrorist detention center now. Fortunately, not even the U.S. Government was supposed to know where the Fridge was. Ward did not find much comfort in that possibility.

John still got plenty of Centipede soldiers left, Deathlok and the rest of Cybertech. But as long as Quinn is locked up here, he's going to need a new face. And of course, John had his own assets within Hydra proper – Kaminsky and his team, for example. Ward could handle Kaminsky and company easily, but that was hardly all John had to work with. And Deathlok...Ward didn't know where Mike Peterson's son was. But he did know where the people controlling the eye implants were. Most of them anyway – Cybertech.

What John really wanted was G.H. 325. And the only people who knew anything about it were the people on his team. Skye and Coulson – they'd have to be the people John would go after.

But with all those samples of everything else he could find taken from the Guest House, John was going to be able to try another angle.

Raina. He's going to free her.

Before Ward could stay on his thoughts, Agent Hand approached him. "I just received word from the Hub. The Cube has been retaken, but the United States Air Force is moving in to take control of the Hub."

"We really shouldn't be surprised." Ward replied, standing as he spoke. "I've never found anyone in the U.S. Military to be happy when S.H.I.E.L.D. claims jurisdiction." He paused, "or anyone, really."

"And now everyone feels like they can get their own back." Hand agreed. "Agent Coulson has enacted the Odyssey protocol. He and the rest of your team already took off."

That was one that Ward wasn't familiar with. "Odyssey Protocol?"

"Complete abandonment of the facility." Hand answered. "From the sound of it, most of our people left in the Hub are willing to take their chances with the United States Government." She didn't sound happy about that, but that hardly surprised Ward.

"What's the official story on Garrett?" For some reason, Ward doubted that she was going to simply log that he was summarily executed by being thrown out of a plane.

"He tried to escape, made a grab for a parachute, didn't manage it, but fell out of the plane in the fighting." Hand answered. "Congratulations, Agent Ward. You managed to make sure the Clairvoyant didn't escape with his life."

The exact opposite. "Alright." Before he could say more, his phone started to ring. Ward looked. It was Coulson. "Looks like I'll get my chance to tell that to Coulson." He opened the phone and brought it to his ear. "Sir? Is everything alright? Hand told me you were evacuating the Hub."

"Hey. It's me." It was Skye on the other end of the line. "Yeah. Not fun, but apparently there's a Colonel Talbott coming for the Hub."

"Glen Talbott?" The Air Force must be really pissed to send him. Well, the Air Force and the entire U.S. Government.

"Yea. Sounded like Coulson knows him."

"He's got a reputation." Ward replied.

"Well, I called to let you know that Grant Ward no longer exists. Coulson's orders. Wipe the entire team from the information dumped onto the web. Scrubbing our I.D.s while Coulson figures out our next move."

That...that was something Ward hadn't expected. Of course, if not being Grant Ward anymore was as simple as wiping files... Still...

"Makes sense." He told her. He was about to elaborate on the 'fate' of John Garrett when Skye replied.

"So who are you going to be now?" She said it playfully, as though it was a joke, but the reply froze on Ward's lips.

Who was he going to be now? S.H.I.E.L.D. agent, or John's man? He'd always been who he needed to be for whatever his circumstances, his mission...he wasn't always sure who or what he was, underneath everything.

After a pause that went on just slightly too long, Ward said "I'm not sure. I'll let you know when I figure it out. Where are you headed? I'll meet you there once I'm done here with Hand." He had to stay by Skye. Keep her safe. That was all that mattered.

"No idea. I'll keep you posted." Skye sounded...tired. No. Exhausted. Ward wasn't surprised the world that she'd just finally come to accept as her own had just come crashing down around her.

Even he was starting to feel fatigue, and he was used to...

No. No one was used to throwing the man they owed everything to out of a plane...and knowing the man was probably still alive, and with a very, very good reason to go after him and the one person he cared about.

No. Not the one person – he did care about the rest of the team...more weakness. But it was Skye that he'd turned on John for. Skye that had been the catalyst. Skye that he...Skye that he wanted. After all this was done, if there was an after, and if Skye was done with the team, the bus, S.H.I.E.L.D...well, he had no reason to stick around either.

"Good. I'll catch up with you when I can then."

"Be careful." Ward had heard that so many times in the past – but until the Bus...he'd never really believed it, except from John. And now...the only person he wanted to hear it from was saying it.

"You too." Ward hung up and looked to Hand. "Skye wiped the team's records."

"I guess that makes you an 0-8-4 like Agent Skye. All of you." There wasn't any disdain in her voice as she referred to Skye as an Agent. Something else he hadn't expected from Hand.

Unknown origin. "Technically, maybe." Ward agreed after a moment. "But only technically."

"From the sound of your conversation, you're not going to be sticking around. We could use a man of your skills to hold the Fridge."

Ward looked at her skeptically. "Do you really think you can hold the Fridge?"

"Until things start to get sorted out? Yes. Right now, its chaos. There's still fighting going on – the opening moves of Hydra's power grab are still playing out. If we can ride this out – S.H.I.E.L.D can regroup. The Fridge is a secure location. Not much else is secure, for the moment."

"Agent Hand, you're deluding yourself. S.H.I.E.L.D. is dead." Ward let a bit of true feeling out. "We're a terrorist organization. Our files have been dumped onto the internet and Director Fury is dead. We have no support infrastructure, no backup, and at least half our people – including the Secretary of the WSC – turned out to be Hydra. What exactly is it that we're going to do?"

"Our job, Agent Ward." Hand's stiff tone told him all he needed to know about what she thought about his words. "S.H.I.E.L.D. isn't just an institution. It is an idea, and I still believe in it. Do you?"

"No." Ward replied. "Not anymore." Never. "After everything that's happened? We're not the 'line between the world and the much weirder world' anymore. If we can't protect our own secrets, can't find secrets like Hydra in our own midst, then we can't protect people from secrets they're not ready to know yet." Ward's real disbelief in S.H.I.E.L.D. was more than enough to make his false reasons ring true.

"And yet you're going to go back to your team. You think they'd agree with that assessment?" Hand clasped her hands behind her back. "Or does some part of you still believe in the ideals of this organization?"

The question wasn't hard. Skye wouldn't – she was too...good. And S.H.I.E.L.D. had become a home for her. A family. She'd come to believe in the idea that was S.H.I.E.L.D. Not all of it, but the fundamentals. Coulson – god, Coulson would never stop believing in that idea. Fitz and Simmons, even after everything, were too naive and idealistic. The only one who might even come to that conclusion was May, and somehow, Ward doubted she actually would.

"No. Probably not. But they're still my team, and they're about the only thing I have left that I do believe in." And one of them more than the rest. "Besides, my marketable skills boil down to lying, theft and murder and being a former member of what is now a terrorist organization means I can't exactly join a legitimate agency. My other option is to go freelance. Becoming a mercenary doesn't sound especially appealing." Which was entirely true. It was an option he'd kept open for years though. And would continue to.

"So you're choosing S.H.I.E.L.D. as your option of last resort?" Hand's disapproval remained evident.

"My choice is my team – Skye, Coulson, the rest. They're going to choose to stay with S.H.I.E.L.D. and so that's where I'm staying, as long as they do." Ward gave a small shrug. "So we're on the same side. I don't see that changing."

Hand didn't say anything for a long moment, then nodded. "After everything that's happened, everyone needs a reason to stick around." She turned around. "Once you hear back from your team, you can take a jump jet to wherever they are. But I don't want you inside this facility again after that. If Coulson has someone or something to deliver here, he can send someone else to bring them."

"Fine." Ward was unbothered. "For what it's worth, good luck." He told Hand. "The Fridge needs to stay secure. The people here shouldn't be roaming free."

"I think we may have run out of luck." Hand replied. "Luck was the only reason Hydra's bid failed, in the end."

"I think Hydra overplayed their hand, myself." Ward countered. "They spent seventy-years rebuilding, and they botched their whole 'out of the shadows' plan. Its one of the first things I was taught as a specialist – use an enemy's confidence against them. This time, we didn't even need to know about it for it to screw them up."

Ward only knew a few details about what the Project Insight carriers had been about, all learned after the fact, but the whole plan struck him as far too elaborate. Too complex. They must have taken the new authority S.H.I.E.L.D. had been given after the Battle of New York and run with it. Let it go to their heads.

And in the process, they'd made Grant Ward's life far more complicated. No – no. He'd done that all himself, by falling for Skye...falling so hard that she was more important than John...and yet still being unable to just kill John and be done with it.

I'll have to be ready for him.

He wouldn't fail Skye again. Never again.

Author's Note: How was it? Think I got into Ward's head right?

If you ever think I've got a character's voice or characterization wrong, tell me – I'm just starting out in writing Agents of S.H.I. . Fanfiction, and so I'm not going to sit here and claim I have these characters down perfectly.