Third person point of view: 

Tony walks into the tower and calls out for Jarvis. "Jarvis check the news cycle. How's Pepper doing with them at Stark?"

Tony received no response from Jarvis and Bruce immediately runs to check on Natasha and calls out over his shoulder. "Go to the lab to check on Jarvis I'm going to check on Natasha!" With how quickly Bruce reacted Tony heads out at a sprint to check on Jarvis, when he arrives at the lab he goes over to the computer.

"Alright Jarvis I know you're tired but come on wake up. Out of sleep mode, we've got work to do." Tony said slightly panicked and rapidly pressing keys on the computer. By the time Tony realized that Jarvis was off his phone was ringing and he pulled it out of his pocket and answered it. 

"Please tell me Natasha is with you!" Bruce said as soon as Tony picked up. 

"No she's supposed to be downstairs with you that's why you went to check on her. I have to deal with the fact that Jarvis somehow got turned off." Tony responded confused. 

"Shit! Get Jarvis back up and call Clint to see if she's with him and then call Pepper, because she isn't here and there is a letter on the  door." Bruce said hanging up the phone. 

Tony began multitasking right away. He had Jarvis back up and running by the time that Clint picked up the phone. "Is Nat with you?" He asked while still typing. 

"No, but she might be in the nursery let me check." Clint said getting off of his and Natasha's bed. He unlocked the nursery to find the utter destruction that Natasha had left and he sighed. "She's not here, but she was, and she destroyed the nursery. Let me look in a couple of places. I'll call you back." 

Clint hung up the phone and Tony threw his across the room. "Fuck!" 

"Tony? What's wrong?" Pepper asked when she picked up after Jarvis had called her. 

"Well. We don't know where Nat is." 

"You lost Natasha!" Pepper screamed. 

"We didn't necessarily lose her. We just don't know where she's at right now." Tony said awkwardly. 

"Tony! What the hell? No this is terrible. Bruce took Natasha to see the baby. Why did you guys leave her alone?"

"Shit! Hold on Pepper. Clint's calling me back I'm going to patch him in." 

"She's gone. Natasha took her go bags and the jet is gone." Clint said somberly.

"Fuck! I'm coming back to the tower. Call a family meeting. I'll be there in 15 minutes." Pepper said hanging up the phone. 

"Clint can you start calling her and casting nets. I think you'd be the one most likely to find her." Tony said typing things into the computer. 

"I'll see what I can do, but if Natasha doesn't want to be found she won't be." Clint said somberly and hung up the phone. He collapsed face down onto Natasha's side of the bed trying to feel her. he laid there for about ten minutes until Jarvis sent a family meeting reminder to his phone and he got up and walked to the kitchen. 

When he got there everyone was standing around the table arguing and Bruce rushed into the room right behind Clint. 

"Clint good you're here. Did Natasha pick up when you called? We've all tried her ten times and texted her even more. We're going to have to call Fury soon." Tony said stopping the commotion to notice Clint's entrance.

"Did you really think she would? I told you she doesn't want to be found so we aren't going to find her." Clint said annoyed and sitting down at the table and putting his head in between his hands. 

"Shit. Bruce did you find anything? Did she leave anything other than the letter." Tony said rubbing his face. 

"Not a trace. I've checked everything. I didn't open the letter, I thought we should all be here when we do. Did you check Jarvis's logs and the security cameras, she had to have slipped up somewhere." Bruce said walking around to where Tony was. 

"No she wouldn't have slipped up. This is Natasha we're talking about guys, like Clint said if she doesn't want to be found, she won't" Sam said breaking his silence for the first time. 

"That doesn't mean we are going to stop trying. We can't stop trying! She has to know that we want her, that we care about her! We have to keep trying, We have to keep looking!" Tony said getting hysterical and sitting down and having projections surround him. 

"Tony, we never said we were going to stop looking, but Natasha can take care of herself, we don't have to worry about her, she isn't a child." Bucky said irritated.

"You think I don't know that! Natasha can take care of herself, but I don't think she's going to, we need to let her know that she has to come back, because I don't think she's going to! We can't lose her!" Tony yelled standing up again. 

"Tony calm down! We need to work together, we need everyone's help, so sit the fuck down and chill the hell out!" Pepper said walking in and immediately taking control. 

"Pepper did you find anything?" Steve asked as she walked over to the projections Tony still had up. 

"I set up a system to start looking for her at Stark, but it's got nothing so far. Happy's watching it for now. The press wasn't bad and no one has figured out she's missing yet so that's great. We need to make a decision. Are we telling Fury or are we just going to wait for him to find out?" Pepper said walking over to take the letter out of Bruce's hand. "Did she leave this?"

"Yeah. I found it taped on the door to hospital wing. I didn't open it, I thought we should all be here when we do." Bruce said handing it over. 

"Well, we're all here so, what are we waiting for?" Tony said coming over to Pepper. 

Pepper tore open the letter and read out loud. "To S.H.I.E.L.D and Avengers. I quit. Don't come looking for me. Signed Natasha Romanoff." 

"She's gone. She's not coming back and we aren't going to find her unless she wants to be found so we might as well just cast the nets and wait. There is nothing we can do anymore. I told you guys this was going to happen, but none of you wanted to believe me! You know what. That's it I'm done. I'll figure it out." Clint screamed, then slammed his chair and left the room. 

The room was silent for a few minutes as everyone processed what had just happened. After Rhodey had had enough of the silence he spoke up. "We screwed up. We shouldn't have all left. She probably thought we abandoned her. Bruce you took her to see the baby which was a bad move. We should have read that letter before we told Clint. I won't be surprised if he leaves now. We need to work on finding her and that means telling Fury. Her letter didn't give us much of choice, she quit." 

"Do you really want to tell him that his favorite agent and one of his daughters just quit and said not to find to find her and then her partner and husband also left?" Bucky said sarcastically. 

"If I have to be the one to do it then yeah. I would have said Clint should do it, but that's out of the picture. I mean we could have you do it, Pepper, but I don't want you facing the wrath of Fury. Bucky he still isn't very happy with you and that also extends to Steve. Tony you're not emotionally stable right now, neither are rest of us, but right now you're the worst. Bruce this is a very delicate situation and those aren't you're specialty. So that leaves me and Sam to tell him, and I think Sam has a slight disadvantage over all of us in this situation, considering the fact that he's dating Fury's other daughter." 

"Rhodey, Fury doesn't know about Maria and I and I would like to keep it that way, so I can have a shot at getting on her good side again. I'll go with you when you tell him. Plus I mean I think we out of everyone have pissed him off the least." Sam said standing.

"You guys are leaving right now? At least give us an hour to find her and bring her back." Steve said trying to stop them.

"Steve we don't know when she left. We've been gone all day. The quicker we tell Fury the better chance we have of finding her. I hate to say it, but right now S.H.I.E.L.D has better resources than we do. They've known her longer and have established some of her hiding places." Tony said sitting and putting his head in his hands. Cap sits back down and tension diffuses as Sam and Rhodey leave in the other jet to fly back to the Helicarrier. 

The flight wasn't long, and they were on the Helicarrier walking to Fury's office in about thirty minutes. As they walked to the office they didn't talk and kept up their facade of confidence in their military dress uniforms. They were let into the office and kept up the facade. Fury is the first one to speak. 

"What're you doing here? I literally just sent you guys home."

"Well sir we have a slight problem with Agent Romanoff." Rhodey said speaking first. 

"What happened?" Fury said slightly apprehensive.

"Well she has resigned from both S.H.I.E.L.D and the Avengers sir." Rhodey continued. 

"What! After all of the work I just did to keep the council off her back, she quit? Get her on the phone right now." 

"That's the problem sir. She's gone. She left a note, she isn't coming back. We were hoping that you could help us find her." Sam said jumping in for the first time. 

"Let me see it." Sam hands over the note and Fury reads it. "Well fuck. I'll cast my nets and try and find her. Keep the council and the press at bay for as long as you can on your end. I'll do the same on mine. Rhodes you can go, but Wilson I need to have a word with you." Rhodey nods and heads out to wait in the hall for Sam to finish. 

Fury walks over to his desk and looks at the few pictures he has on it. "Sam you need to step up. I don't know how long Natasha is going to be gone for and if she comes back I don't know to what capacity she will be working at. You've got to help out Rhodey and Steve to try and cover the hole Natasha left. To do that you have to fix the whole Maria situation that you got yourself in. And don't try to deny it I've known about it since the beginning, there's very little that goes on with my daughters that I don't know about. And before you ask Maria did not tell me." 

"Sir, I'm sorry. We didn't think that you would find out. I wanted to tell you, but Maria said it was a bad idea." 

"At least you have the brains to apologize. I'm fine with you dating Maria, honestly I've been trying to set her up with someone for years, she's too uptight. But Wilson, listen to me. If I ever so much as get a whisper about you hurting Maria, just know that the last person to hurt Natasha has never been heard from again."

"Understood sir. Thank you." Sam said shaking Fury's hand and leaving to go meet up with Rhodey. 

"What was that about?" Rhodey asked when they were on their way back to the tower. 

"Fury knew about me and Maria the whole time." 

"How much shit are you in?" 

"Surprisingly not that much. He said he was fine with me and Maria."

"Wow OK. You better savor this because as soon as this fiasco with Natasha and everything dies down, he's probably going to change his mind." 

"What no. He seemed fine."

"Yeah it's because he's preoccupied with his other daughter. He doesn't really have time to worry about who Maria is dating at the moment."

"Well I might not even have to worry about it either. Me and Maria got into a huge fight a few days ago she hasn't talked to me since." 

"You should call her then. Tell her what happened with Fury and Nat and everything. Tell her you're sorry because I know you love her." Rhodey said after a few moments of silence. 

"Pepper?" Clint asked quietly after finding her alone on the couch after the meeting. She was on her phone repeatedly checking her texts and sending messages to Natasha and Happy simultaneously. 

"Clint? Is that you? Come here." She said trying to get him to come closer. 

Clint obeyed and walked towards her. When he came closer she could see the tear stains and bags under his eyes. She could also see that he had his mission bags packed and with him along with his bow. "Your leaving aren't you? You're going to look for her." 

"I need you to finish making the funeral arrangements. I need you to set a date and let me know when it is because I can't do it. Natasha... She's. She's not going to come so don't worry about that. I just need you to do this for me, whatever you decide is fine with me. I don't care, as long as you tell me when it is so I can be there." Clint said with a few stray tears falling from his eyes and avoiding the question. 

"Clint. That didn't..."

"Please Pepper. I need you to do this for me. Please. If you need me I'm only a phone call away, but I'll only pick up for you and Coulson right now. I've got to deal with this my own way for right now. Natasha she's gone. She left me and I don't think..."

"OK Clint I'll do it but, don't say that. Natasha, she's dealing with this in her own way too, you've got to see that. She loves you Clint. She wouldn't have stayed this long if she didn't." 

"We'll see. I've got to go. I'll see you later Pepper. Let the other guys know what happened, please?" Clint said giving her a hug and walking away.