A/N - I really wanted to get this out before season 5 premieres because when it does, this will almost certainly become AU. I suppose it already is, a little bit, because in this story, we do not lose Shaw in the basement of the stock exchange.
What if John disappeared instead?
This story takes place sometime between "Control-Alt-Delete" (4x12) and "Asylum" (4x21) It will, ultimately, give one idea on the closure of the Samaritan timeline.

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April 9th
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"Miss Shaw, I really must insist that you stop purchasing these 'cow femurs' for Bear."

"But he likes them, Finch."

"Yes - that may be. However they do not like him. At least this particular brand. Perhaps you could try something organic?"

"Are you kidding? Organic? Organic just means it's got bugs in it, Finch."

"Then something with fewer chemicals? It really does wreak havoc on his digestion."

"Well - then make Reese clean it up - Bear's his dog, after all… Where is Reese anyways?" Shaw looked around the subway - she hadn't seen Reese since their last case concluded a day and a half ago.

Finch glanced up from where he was watching Bear devour his latest toy and looked at her with some concern behind his gaze. "I'm not sure if he made you aware of it, Ms. Shaw, But Mr. Reese sustained some injuries in our most recent activities. With that on top of the fact that he's had very little opportunity for sleep over the last week, I requested that he take some down time to recover - at least until our next number."

Sameen frowned to herself. Reese had managed to keep his injuries from her and she was usually pretty good about noticing such things. It was important to be aware of your teammates' battle readiness - especially now that Samaritan seemed more powerful than ever. It certainly wasn't because she cared…

She looked back at Bear, who appeared to be having the time of his life, and sighed. "I'll be more careful about reading labels in the future… okay, Finch?" When he didn't respond, she looked back at him. He was frowning at his phone. It seemed he had received a puzzling or worrisome text. "Finch?"

He kept frowning and held out the phone toward her. "I just received a text from Mr. Reese. It appears to be some kind of code, but I have to confess, I don't know what it means. Do you?"

She shrugged and took the phone from him. She looked at the screen. It held three seemingly random letters. They formed no word.

She gasped. She froze.

"Miss Shaw?"

Sameen stared at the screen of the phone. She knew exactly what those letters meant and it felt like a punch in the gut.

Which was strange. She didn't usually have reactions like this.

A punch in the gut. In a fight, she prepared for those and they barely left a bruise. But if someone managed to catch her unprepared… It hurt - it was a shock - and it left her gasping and nauseous - which was exactly how she felt right now.

Finch felt the first tendrils of panic grab at him when she did not respond to his inquiry but continued to stare, unmoving, at his phone. "Miss Shaw?!"

Miss Shaw didn't normally do emotional reactions. The fact that he was clearly seeing one now caused him no end of worry. "Sameen." He prompted softly, but urgently. "What is it? What's happened?"

Shaw realized that Finch was waiting for an explanation of John's text, But she was loathe to give him one. She shook her head at how smart - and how cruel John was to send this text to Finch's phone; a text that only she would understand. Her hand holding the phone dropped to her side and she stared at him. "Reese was burned by the Agency, right?"

Finch blinked. "You could say that..."

"So you know what that means."

He tilted his head, worried. "The Agency basically turns their back on you. You are 'fired' in the most graphic of ways - forgotten - abandoned… it nearly always means the agent has been - or will be - captured... or... killed… In John's case it was the latter. The Agency tried to wipe him off the face of the planet." He was becoming increasingly uncomfortable with the course of this conversation. He very nearly didn't ask, "Why?" He was pretty sure he didn't want to hear what she was going to say.

She held up the phone towards him. "Are you absolutely sure this is from Reese?"

"It is from his phone, yes…"

Her arm and her eyes fell. "Then... we've lost him." She said- her voice completely without emotion.

He took one step toward her. "What do you mean… lost him?"

She looked down at the phone in her hands and spoke quietly. "This is a burn code." She was surprised that she needed to pause and swallow before explaining. "It's something an agent will set up with his team. It is a way to… 'burn' yourself... If the situation warrants it - if you know absolutely that you cannot survive or be saved - and any attempt at rescue would be suicide - you can… 'burn' yourself." She swallowed. "This is John's burn code. He's telling us he's not coming back and not to come after him... that he's lost to us - that something has happened and we cannot save him."

Finch could not accept the information being shared with him. "That's ridiculous." He said dismissively. "It's someone else using John's phone - trying to throw us off - we have to find him!"

"Finch." Shaw rested a hand on his arm as he quickly sat and began to type. "It's not. It's John."

"How can you be sure?"

"Because he set the code up with me. He and I are the only two people in the world who even know the code exists - much less what it is. And if you think someone managed to trick him into sharing it? Or tortured it out of him? No way. It's from John."

Finch's eyes were darting back and forth - he was very nearly in a true panic. "He knows we won't listen - that we'll come after him anyway - that's what he did with me. More than once I gave him every reason - I tried to keep him from coming after me and rescuing me. Nothing stopped him... Nothing will stop us now." The purpose gave him some measure of calm and Sameen hated to crush it.

The truth was she was feeling conflicted. On the one hand she knew John hadn't sent the code lightly. He would not have sent it unless he truly believed it was necessary - and John was usually right about such things. On the other hand - she was just as desperate to go after him as Finch. If it was just her, she would already be gone, but she also owed it to John to make certain that Finch was safe.

She decided on something of a compromise.

"Harold." She pulled up the opposite chair and sat facing him. As much as she hated it, she had to get him to listen. "You're right. John knows you won't stop looking for him. That no matter how dangerous he tells you it is, you'll try anyway and probably get yourself killed. No - actually - In light of this code - you would get yourself killed. And probably me too - and Root - Fusco - Bear… Anyone we involve. That's why this text isn't really directed at you at all... It's a message to me."

The last sentence was spoken with such despair that Harold finally stilled and really listened to her.

She was glad to see it - but also saddened. When she spoke, she couldn't meet his eyes. "Finch - you know how much I hate to admit it, but overall- Reese is better than me. He's more skilled in many aspects of our work." She looked up at him. "And he knows us… knows my training, what I can and cannot do. And he is telling us that this is beyond our skills. Whatever it is - we can't beat it. And yes - he knows we'll try anyway." She cleared her throat. "By sending a message to ME on YOUR phone… He's asking me to keep you from trying."

"But you won't do that - you will not abandon him…" Finch implored her.

But she leaned forward and looked him in the eye evenly. "Yes. Finch. I will." She held up the phone once more. "This is a last request, Finch. This is a request from a dying man - from a friend. I owe him. You can bet your life I will honor it. And betting your life is exactly what you would be doing if you cross me."

"Sameen…" Finch was beginning to see that she was actually serious.

Knowing she had him listening, she gave him some hope. "But that does not mean we are going to forget him." Shaw continued. "We can't launch a rescue mission right now, but we aren't going to sit on our hands either. We can start by trying to figure out what happened.
I'm sure his phone's been destroyed by now, but where was he when he sent this?"

Finch stared at her for a split second before leaping into action. It only took him a moment to pull up the GPS records on John's phone. "The text was sent from his apartment."

"Let's go."

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Finch and Shaw arrived at John's apartment in record time and Shaw entered warily, gun drawn and ready, Bear at her side. Finch followed cautiously.

They found absolutely nothing. John's apartment was neat and quiet. There was no sign of a struggle, no clue as to what might have happened.

Shaw holstered her weapon.

"What now?" Finch asked.

She sighed. She'd really hoped they would find something to let them know if he was even still alive. "I'll take a spin around the neighborhood with Bear. See if he can pick up a scent. You head back and work your computer magic. See if you can hack security feeds around the building… you know the drill."

He nodded, discouraged and worried, and left.

Finch had known from the very beginning. ""We'll both wind up dead… really dead this time." But to have his prediction come true was far more painful than he'd expected. And to have it come true now - when things were the darkest they'd ever been. When Samaritan was growing in power every day… If John was really dead, then Finch feared it would not be long before the rest of them followed.

A few hours later they were both back. Neither of them had found anything useful. Even Bear had found no trace of his scent outside his apartment building. It seemed that John had simply disappeared.

"Do you believe he is alive?" Finch asked her in a small voice.

She gritted her teeth. "If it is humanly possible to survive. John will. We need to hold onto that." She looked at Finch, suddenly feeling more alone than she had in a long time. "And we will not stop looking." She also felt a new sense of resolve. John had always been the protector, where she had been something of a loose cannon - allowed to be so by the very stability John provided. That would change now. She would protect Finch, and their mission, with the same fierceness John had.

She silently made her vow to him - wherever he was.

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TBC…
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