Y/N stayed at Avengers Tower, under the watchful eye of Tony, until she was completely healed. After that, Maria Hill and her started coordinated with Coulson on trying to find Loki's scepter. Y/N was honest with Tony about what she was doing, though insisted he stayed out of it due to needing to keep Coulson a secret. Tony was understanding about it all.
Y/N made frequent trips to the new hidden SHIELD base, trying to get the new SHIELD up and running. Under the direction of Director Coulson, Y/N was made his right hand. Which made people a little mad. Coulson was changing, becoming more secretive. He was hardly ever at the new base anymore. The original team members didn't like that. But Y/N new it was for good reason. Coulson was trying to find Loki's scepter and he had found a helicarrier and was trying to get it repaired. They were also keeping a secret about Simmons. Currently, she was undercover at HYDRA, only Coulson and Y/N knowing. They had made it seem like she left SHIELD. This took a tool on the team members, especially Fitz.
Y/N drove into the hanger ready to start another week at SHIELD. It had been a few months since the fall of SHIELD, and Y/N made sure to balance it and her relationship. She parked, grabbing her duffle in the passenger seat before stepping out.
"Look who decided to come back," Mack teased, walking down the ramp of the Bus. Mack had been a SHIELD agent then was recruited to help them rebuild. "Sure missed you around here."
"Missed you too, Mack," Y/N smiled. "Things fall apart while I was gone?"
"No more than usual."
"Great, well I have a meeting with the Director that I'm already late for. So we'll talk later."
"Good luck," Mack wished as Y/N entered the base.
As she walked down the hallway, Skye came walking the other way.
"Y/N!" Skye smiled, coming up to hug her friend.
"Hey, Skye," Y/N hugged back. "I've only been away for a couple of weeks. You missed me that much?"
Skye laughed as she pulled away. "Of course. You're the only one around here that actually tells us what's going on."
"Yeah... Coulson in his office?"
"Where else would he be? He's currently got May up there for debriefing."
"Awesome."
"Tell him that I want to talk."
"Of course."
Y/N made her way up to Coulson's office, where May and him were already talking.
"Talbot's saying he's beaten both sides," Coulson was saying as Y/N entered. "But we're just hiding underground. If HYDRA gets their hands on this, they may not have to."
"What are we worried about now?" Y/N came further into the room.
"Agent Rogers, thank you for coming so quickly."
"You called, I answered, Tony wasn't very happy."
"You handcuff him to a bed frame again?" May asked.
"No. Just left while he was sleeping. It's not that he doesn't know what I'm doing here, he's just been clinging since the accident. Which is understandable. But, what do we got here?" Y/N picked up the old SSR file that laid on Coulson's desk. "An 0-8-4?"
"The first," Coulson replied. "And we need to find it before HYDRA does."
"Awesome." Y/N nodded.
"I want Hartley and her crew up here for debrief. May, you check on the lab, see where they're at with the metal you found."
"How is he? Fitz?"
"He has his good days and bad days," May replied. "I don't know which one today is though." May walked out.
"You need me, boss? Or can I unpack and await orders?"
"You can unpack," Coulson answered. "And, you might want to check in with Fitz yourself. He might cheer up upon seeing you."
~~~
Unpacking didn't take Y/N very long. She tried to keep a lot of her needs things on the base. She grabbed a few bottles of beer before heading to the lab, where she found Fitz alone. He was frustratedly running a hand through his hair. It was hurting everyone to see Fitz like this. Ward tried to drown Fitz-Simmons. To safe Simmons life, Fitz forgo oxygen, causing him to have a traumatic brain injury. He was slowly getting better, but still struggled to form sentences.
"Hey, Fitz," Y/N smiled, walking up to him.
"Y-Y/N," Fitz greeted with a stutter, not moving from what he was working on.
Y/N sighed. This wasn't unfamiliar territory to her, she was dating a man that spent most of his time hutch over something in a lab. It just hurt to watch them do it, trying to find a way to fix or ignore reality.
"I brought some beer," she told him. "I thought that you might take a break with me."
"Can't," he answered. "I'm trying to um... I've been trying to get... uh..." He snapped continuously as he tried to form the words. "Yes! I'm trying to figure out cloaking for the Bus."
"Do you need help?" Y/N moved closer. "I've spent enough time with Tony in his lab to probably led a useful hand."
"N-no... I'm fine."
"Can I at least stay and watch?"
"I said I'm fine!" He shouted, throwing what he was working with off the table. "Just leave! I don't need your pity..."
"Fitz," Y/N reached out but her hand was swatted away.
Fitz walked away, leaving Y/N standing in the middle of the lab.
~~~
Y/N found her way into the Bus' command center, where her and Skye were trying to figure out some drawings Garrett had been messing with. Skye was laying on the table while Y/N was standing, leaning up against it, staring at the screen.
"It's a little bit strange," Tripp said as he entered, carrying a beer for each of them. "I mean, they're exactly the same." Skye sighed as she sat up. "You really think they were just twins? Come on."
"Are you on about the Koenig's again?" Y/N asked as she took a beer.
"I've heard all your theories, Tripp," Skye said, taking a beer and drinking it.
"And Koenig's always mentioning other brothers," Tripp continued. "Every day, another bright. If he bring up one more brother, I don't know what I'm gonna do."
"Coulson said we can trust him."
"There's something fishy going on there, man." He took a swig of his beer. "You two will go crazy staring at this crap. What is it again?"
"Not sure," Y/N replied. "Something Garrett was messing with."
"Coulson put us on it a month ago, searching deep web contacts," Skye explained, sliding off the table, "even Rising Tide and Stark's database, looking for a match. We've got nothing."
Tripp chuckled, "There he is." Both the women turned to see Coulson headed in their direction. "Happy to see you, sir," Tripp continued.
"Agent Triplett, Skye," Coulson greeted.
"Sir," Skye greeted in return.
"Can you give us a moment?" The Director asked Tripp.
"Watch this," Tripp responded, quickly taking his leave.
"What? No hugs?" Skye teased. "He was really looking forward to it."
"We've cross-checked the writing from the lab with the new images you've given us," Y/N explained, immediately thinking he was here for a debrief on their assignment.
"Mostly the same," Skye continued, "but the code breakers haven't found anything-"
"That's not why I'm here," Coulson stated, handing each of them a paper. "The bulletproof assassin encountered on the sting? We know who he is."
"You want one of us to go down there, don't you?"
Y/N tensed. She hadn't faced Ward since he shot her in the back. And Skye hadn't faced him either. But, for some odd reason, he insisted on only talking to Y/N or Skye. He also offered to talk to Fitz. But for Fitz' own good, he was not informed about Ward being on the base. No one could get information out of him otherwise.
"You two are the only ones who can," Coulson said.
"Is this really what it take for you and I to talk these days?" Skye wondered. "Why now?"
"Because the technology at play warrants it."
"And do we have a say in this?" Y/N asked. Coulson simply responded with a sigh.
"Copy that," Skye replied.
The two women headed into the base.
"I think we should go together," Y/N said, quietly.
"I think so too," Skye responded.
They met up with Agent Billy Koenig, to go over the security measures where Ward was in the base.
"There's an inertial confinement laser barrier down there," Billy explained as they walked, "which is cool." He had a tablet in his hand, showing the women how to use it. "Now, this button turns it soundproof, this button makes it opaque."
They stopped in front of the door. Y/N stared at it as Skye was handed the tablet.
"Just tell me there isn't an off button I can accidentally hit," Skye said.
"Or a kill switch," Y/N murmured.
"You guys will be safe," Billy reassured. "I promise."
The two women looked at each other, seeking comfort from one another before they opened the door. They headed down the dark stairs, everything slowly lighting up as they did. The light allowed them to see Grant Ward, behind an electric shield, shielding his eyes from the light.
"Are you two a sight for sore eyes," Ward said with a small smile.
The women were stoic. Skye sat down in the chair as Y/N stood, arms crossed, behind her.
"I told Coulson weeks ago that I was willing to speak to you two," Ward said. "To give you intelligence. Why now? Something bad happen?"
Y/N tried to conceal her anger at his fake concern. Just being down here was enough for Y/N to have the urge to use him for targeting practice.
"Carl Creel," Skye stated, getting straight to the point. "Garrett reported him dead, turns out he's alive. Do you have any information on that?"
"How've you two been?" Ward asked. Skye stood up, turning to leave. "The name sounds familiar. Do you have a picture?"
Skye pulled one up on the tablet before turning around and moving to show Ward. He inched his face as close as he could, allowing the energy shield to show itself. As he did, Y/N caught eye of his wrists and forearms. There were scars there that weren't before. Ward noticed where she was looking.
"Coulson didn't tell you," He stated, looking Y/N in the eyes. She quickly looked away. "I went through a... rough stretch. The first pair of pants they gave me had a button on the back. They took that away, but you fold a piece of paper just right, it gets sharp. And when they took that away, I started running at the walls."
"You should have ran faster," Y/N growled.
"I'm through all that. When I came out of sedation, I was clear-headed. Accepting... Of who I am, what I've done, and why. Now, Skye, your arms tell I different story. I see May and Y/N have been training you. May's got you favoring your left side first cause you're right handed. Smart."
"I'm gonna say this once," Skye began. "I'm not gonna believe a word that comes out of your mouth. But if a single word is about anything other than the question that we're asking, we walk."
"Okay." Ward held his hands up, taking a few steps back. "Creel was a boxer, nicknamed the Crusher. Turns out any opponent has a glass jaw when you have still fists under your gloves. Garrett thought he'd be an asset. Now, once Creel touches a substance, he can absorb it and somehow consciously transform the molecules of his body into that substance. He wouldn't tell us how. But he enjoys the way it feels. Almost as much as he enjoys killing."
"You two must've gotten along great," Y/N responded.
"Well, this was fun but pointless," Skye said. "We've already figure that stuff out." Skye turned to leave again. "SO if you don't know where to find him, then-"
"Wait," Ward called out. Skye didn't bother to turn back around. "When HYDRA was communicating within SHIELD we'd use white noise in the gaps between SHIELD's quantum key distribution channels to hide messages. And SHIELD might be gone, but not those frequencies. If HYDRA is giving commands to Creel, that'll be how."
"We'll see."
"It's true. And so will be every word I say to you two for the rest of my life. I'm not asking for forgiveness. I just wanna help you, the both of you. And when that information proves true, I hope you two will come back. There's so much I wanna tell you about-"
Then Skye cut him off, using the tablet. They left the bunker and headed to Coulson's office. There they found May, Coulson, and Billy in there.
"-how many HYDRA agents can communicate this way," Billy was finishing up.
"So he's telling the truth," Skye stated.
"It looks like it," Coulson replied. "Thank you."
"I guess that visit was the first of many, huh?"
"We kept Ward here for this reason and it's paying off."
Skye sighed. "What is his deal?"
"I really don't know. But it doesn't matter. As long as he's giving us an inside look at HYDRA's operations.
"Yeah, guys," Billy started nervously, "about that..."
They all turned to face the screen. Panic started rising in Y/N's chest as more and more red dots found a home on the screen's map.
"You called it," May said. "Talbot hasn't crushed HYDRA. Just sent them slithering back to the shadows."
"I hate being right," Coulson said.
Y/N felt a panic attack coming. This was too much for one day. Her breaths started getting heavier as she backed up. She rammed into the desk behind her, causing everyone to turn and face her.
"Y/N," Coulson called out.
But it seemed distance to Y/N. Unable to answer, she shook her head and stumbled out of the room. More distant voices were heard behind her as she clumsily made her way down the steps and rushed to her room. As she rushed, she brushed past Fitz.
"Y/N?" He called.
She ignored him as she slammed her door shut and locked it. It was instances like these, that Y/N was thankful Tony upgraded her phone.
"JARVIS?" She panted. "Call Tony... please."
"Of course," JARVIS responded.
Y/N slid onto the floor, gasping for air.
"Honey," Tony was clearly already worried. "J said that something was wrong. What happened?"
"I- he- they-" She panted, unable to form coherent sentences. "Tony," she cried.
"It's okay, honey, I'm right here. Listen to my voice. I need you to calm down in order to tell me what's wrong. So listen to my voice, focus on it."
"Tony," Y/N whimpered, trying to calm herself. "I saw him."
Tony was unresponsive for a second. "Do you mean... Ward?" He growled, clearly angry.
"Mhm," she hummed.
Tony was the only one who know about the nightmares that plagued Y/N. She had trouble sleeping ever since she woke up after Ward had shot her.
"They..." Y/N swallowed. "They needed information... He will only talk to me and Skye."
"Then where was Skye?"
"With me... we went down together..."
"Coulson shouldn't have made you do it, either of you."
"And then... the information he gave was right... HYDRA's lurking everywhere, in the shadows... they're no where near gone."
"Well, you're not alone in fighting them. The team has been working on finding HYDRA as well, especially to find what they stole from SHIELD."
"I know... it's just... this is never going to end... they're just going to keep fighting back... everything we've fought for, everything we've done to try and put them down..." Flashes of Y/N falling from the plane back in 1945 played in her mind. "It doesn't matter..."
"Yes, it does. Everything that you've already done to stop them as put a dent in them, pushed them back. Your fights weren't for nothing."
"I just... they're going to make me go down there again... and I... I can't promise I won't kill him..."
"If you do, I'll stand by that decision... I love you, honey."
"Yeah, I love you too."
~~~
The team discovered that General Talbot was endangered. So they quickly headed off to DC. Tripp slipped a phone in Talbot's pocket as he bumped passed him. Coulson called it, instantly putting Talbot on alert, and warned that he was in danger. May and Y/N were out observing, watching for Creel. They both began running when the noticed Creel behind Talbot.
"Watch your six!" May warned. She ran up and kicked Creel in the chest. Causing him to fall back onto the ground.
Talbot's security team soon pulled up, armed and ready as they made their way towards everyone. Creel tore off a ball and chain from some path markers. The brass coloring extended up his arm as May and Y/N stood in front of him. He began swinging the ball and chain at the two women, who easily dodged the attacks. They both kick him down as Skye, hidden in the park, shoots Creel. The two shots hit Creel's chest and electricity sparked between the two pieces, dropping him to his knees. May and Y/N, with Skye too, quickly made themselves disappear.
Hartley and Hunter, disguised as soldiers, usher Talbot to what he believes he safety. They usher him into a black SUV, where both May and Y/N are already waiting. Talbot got in and shut the door before turning to see who's beside him. May had a gun pointed at him while Y/N was in the back, smirking.
"Hi, again," May said.
"Son of a bitch," Talbot muttered as they sped off.
"Nice to see you again, General," Y/N greeted.
"And here I thought you had stopped helping these guys after getting shot," Talbot glanced back at Y/N. "Guess I was wrong."
~~~
They brought Talbot onto the Bus, forcing him out of his uniform and tying him to a chair in the interrogation room. Coulson went in to get information out of him, specifically his finger prints. May, Billy, Skye, and Y/N were watching from inside the Bus' command center. Y/N, sensing that someone was watching them, turned towards the door. There she saw Fitz, muttering to himself. She sighed, he'd been doing that more and more since Simmons left.
After getting most of what was needed from Talbot, Coulson used an icer on him. They left him in an car with a phone, that connected straight to Billy. Everyone was prepping for the mission, they were going to break into that base. Most of them believed that they were going in for the 0-8-4, but it was more than that. They were in need of a quinjet, so the plan was to steal one of those as well.
"We have a small logic question," Hunter came up to May and Y/N. "Why? Why are we going in?"
"Look, we trust Coulson's judgment," Hartley clarified.
"We do?"
"But Talbot's not a bad guy. And last I checked the US government is one of the lesser evils. So they've got the weapon in a locked box. And now they've got this absorbing man in a locked box, too. That's not so bad."
"She's got a point," Mack agreed. "It does seem as safe a place to keep them as any."
"They have no idea what they're dealing with," Skye retorted.
"Yeah, but is that danger worth the risk of sending every field operative you have available into a secure military compound?" Hartley wondered.
"Yeah, guarded bu the same people that've been hunting us," Mack added.
"Belly of the beast, man," Idaho, one of Hartley friends, said.
"Well, we're already on our heels," Hunter said. "We can't even get this thing out of the hangar."
"Exactly," Coulson said as he entered. "This is a make or break moment."
"For an object we have zero data on."
"That's not the only thing we're after." Coulson and Y/N shared a look.
"Now it's all or nothing, huh?" Hartley asked. Coulson merely shrugged. "Well, all right, then."
Hartley and Hunter turned away. Y/N and May begin to walk away, Skye quickly following.
"Which of you two are taking point?" Skye asked.
"Coulson will be on comms," Y/N replied.
May turned while walking. "Hey, let's stick together on this one," May said to the other two, as she walked backwards.
"You got it," Skye responded.
~~~
Tripp was dressed up like a General and they had Y/N dressed up in a pant suit. They were going to use them to get inside. Idaho drove the SUV up to the guard station, rolling down his window.
"I have General Jones and his party here to meet with General Talbot," Idaho told the guards.
The soldier at the window looked at his tablet. "General Jones?" He repeated.
Idaho unrolled the back windows, revealing Tripp and Y/N. Tripp was sitting there, talking on a cellphone. The soldier saluted him.
"Sir," the soldier greeted. Tripp saluted back. The soldier looked behind Tripp to see Y/N. He stood up straighter, saluting again. "Ma'am."
"At ease, soldier," she smiled.
The soldier quickly went back to looking at his tablet. "I'm sorry, sir, ma'am. I don't have the visit in the register today."
"You might want to double check that," Idaho suggested.
"If it's not in here, there's nothing I can do." The soldier pointed in front o them. "Exit to the left, please."
The guard in the booth behind the soldier, tapping against the glass as he's on the phone. The soldier that had been talking to Idaho took the phone. Coulson was back at the base pretending to be Talbot over the phone while getting information from Tripp. Their two cars were waved through and they went straight to a warehouse on the base. They drove one of the SUV into the warehouse.
"Stay and keep it running," Y/N ordered Idaho as she exited the vehicle. "Just in case we have to abort."
"Got it," Idaho responded.
They all look around the big open room, filled with rows and rows of stacks of boxes.
"Needle in a haystack," Hartley commented. "Turns out I was not exaggerating."
"Alright, we know what we're looking for," May said. They all walked in different directions except for Skye, May, and Y/N. "Don't we?"
Then they each separated. They each looked up and down each row.
"I've got the 0-8-4," Hartley said over the comms. "Repeat. I've got the damn thing. Southwest side."
Not long after, Hartley was heard screaming. Everyone rushed towards the sound.
"I can't let go!" Hartley shouted.
She was holding the 0-8-4 in her hand, and something was happening to it. Suddenly, an alarm began blaring.
"Okay, Hartley, just relax your hand," May advised.
Y/N and Skye were watching the metal of the 0-8-4, noticing how the symbols Coulson had them studying appeared. They quickly looked at each other.
"I can't let go," Hartley repeated. What ever the object was doing to her, was crawling up her arm. "Don't touch it," she pushed Hunter away. "Just stay away."
"They'll be on us any second," Skye said.
"Okay, time to go," Hunter decided. "Help me get her up. Can you walk?"
"I think so," Hartley answered.
"What are you waiting for?!?" Hunter looked up at the rest of them. "We need to get her out of here before we all get killed! We got what we came for!"
"Not everything we came for," May stated.
"Wait, what are you talking about?"
"Coulson," Skye called into the comms. "Hartley has the time, but it's attacking her. She needs medical right now. Do we abort?"
No answer.
"Should we just cut our losses?" Y/N asked into the comm. "Coulson?!?"
"Come on! Come on!" Hunter urged.
"Sir, I repeat, what are our orders?" Skye asked. "Do we go dark?"
"Negative," Coulson replied. "Do not abort. Proceed as planned."
Skye, Y/N, and May shared a looked.
"You heard him," May said.
"Help me up," Hartley panted. "I can follow."
"Are you mental?" Hunter questioned.
"We have our orders."
"Screw the orders. We need to get you to a doctor." He pulled her free arm around his neck, lifting her up.
"Hunter-" Skye called.
"No, no. stay her and die if that's what you want to do, but I'm making sure she doesn't." He started down the row as Hartley groaned. "I wish you the best of luck, really, but we're out of here."
Voices of soldiers started entering the building. They began to fire at them. They began firing back as they make a run for it. Tripp, Skye, May, and Y/N started for the quinjets. May and Y/N jumped on motorcycles, distracting the soldiers until Tripp and Skye took off with a quinjet, enabling the cloaking. Y/N and May sped off.