A/N: Thanks for all the reviews for the last chapter. I finally replied to them all before publishing this chapter! Filling the gap between seasons took me a while, but it seemed to work out ok.
Beta by Captainrick944, as usual. Thanks, my friend.
This chapter covers the last month and a half of the gap between Seasons 1 and 2, followed by a rewrite of "Chuck Versus the First Date," the first episode of Season 2.
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Chapter 12: Beginnings and Endings
August was a strange month for Sarah. With no Wienerlicious to work in, she spent it either in Casey's apartment or the bedroom she shared with Chuck. She didn't want to go to the city's CIA or NSA offices.
She found herself waiting for her boyfriend to come home. She hated that. It made her feel like a needy, dependent person, something she had never been.
She often talked to Stephen Bartowski. Sometimes just about the new Intersect, sometimes other things.
Stephen had completed the modifications for the system and tested them as best he could. He explained what would happen to Sarah in one of the calls. "When the new server system is activated, the modified code will immediately get implemented. When downloaded into an operative's brain, it won't hurt them but will erase the last thirty minutes of their memory before degrading itself and knocking them out. When they recover, they will have no memory of the download and no trace of the Intersect."
Sarah spoke next, "Impressive. Can I ask you something, Stephen?"
"Go ahead, Sarah," he replied.
"Do you think you could remove the Intersect from our heads?"
He pondered what to say for a while. "Sarah, I have been working on that for a few months. I think I can, but it isn't as easy as this one here. In this, I have built the removal code into the module I have added. I don't have that in yours."
"But you could build it into an update, couldn't you?" she said.
"I could. Is that what you and Chuck want?" Stephen asked.
Sarah replied honestly. "I haven't talked to Chuck about this, but I think removing it will mean the NSA and CIA will lose interest in him and will no longer see him as their asset."
"And what about you, Sarah?"
That was an easy answer for her. "Oh, I don't want it, so I would like it removed as well."
"That's not what I meant," he replied. "Will you leave Chuck?"
She vehemently shook her head. "I am never leaving Chuck. If I can't work from here, I will leave the CIA."
He smiled, but there was sadness in his expression. "I wish Mary had done that."
"Do you want to talk about her?" Sarah asked. "Or would it be better with Chuck here?"
"Maybe with both of you. You can help him understand what happened."
She nodded. Then, she thought about that Intersect removal again. "When the Intersect is removed, will we lose our mind link?"
"I don't think so. That was additional code. Do you want that removed too?"
"No!" Sarah surprised herself by shouting that. "No, we want to keep that. I think we'd both feel like we'd lost a key part of ourselves."
He nodded and said he'd make sure that wasn't removed, if he could.
By early September, the underground base was complete and fitted out, including a fully stocked armory.
The yogurt shop opened and provided Sarah with a new outfit. She now wore an orange tank top, white capri pants, and a pair of orange Chucks.
Chuck admired how she looked in their bedroom before she set off that first day. "Obviously, you look stunning, as you do in anything you wear." That earned him a kiss. He didn't have to say any more, but did, "I will miss you in that skirt, though."
She grinned at him. "Oh, don't worry about that. I've held onto a couple of those outfits. I know how you like seeing my legs in them."
He really did. "And the skirt flips up so easily," he said.
She pretended to look shocked, but that didn't match what she was thinking. "I'll wear it someday… without panties."
He growled and would have closed the distance between them, but she quickly ran out, saying, "Got to get to work!".
She waited for him in her car, so they could travel together. Neither said a word about that uniform, but both were looking forward to when she wore it again in the privacy of their bedroom.
Sarah's first day as the sole person in the Orange Orange felt weird. She was, in effect, the manager. It was great that Scooter was no longer a problem, but at times the emptiness of the place felt strange. Yogurt was not as popular as burnt sausage meat, it seemed. This was good as it was less restricting, but she had gotten used to the noise of people in there with her,
Of course, Chuck came over when he got a chance and sampled the yogurt. She happily brought him a few samples as they sat and talked.
She then took him around to the freezer. He was impressed with the biometric security and amazed as she took him down into the new base, which they were going to call Castle. The array of monitors on the wall, some large, some small, was impressive. As she took him on the tour, he was repulsed by the contents of the armory, impressed with the training room, and he could see her excitement as she looked in there. The cells and secure access looked good too. All in all, this was some base, especially for a team that only had days left if Chuck got executed.
"Looks like you and Casey are set up to stay for some time," Chuck commented. He was right. It did feel like that.
Sarah said nothing about the timing of the place being set up. "Yeah. Looks like you're stuck with us."
"I still want this Intersect out of my head, though," he replied. They both knew his dad was working on that.
"I better get back to the Buy More," he commented.
Sarah and Casey got summoned to the main room in Castle and faced the large monitor that showed Beckman and Graham.
"We have an urgent mission for the team," Graham told them.
"There was a break-in at the NSA lab. An important artifact was stolen," the general told them.
Graham added, "It's called The Cypher, and we need it back as fast as possible."
"You are the best team to get this," Beckman stated. "You might need to use the Intersect."
The two agents looked at each other. They hadn't taken Chuck on a mission for over seven months. They both knew how much he would welcome this.
"So, after nearly eight months, I'm being asked to go on missions again?" Chuck asked incredulously.
"Yeah. Don't sound so happy!" Casey snapped back. Chuck could read Casey's excitement at having a mission again after so long.
"So, what are we after?" Chuck asked.
"It's called The Cypher."
"The, with a capital T?" Chuck mocked. "Could it have a more ridiculous name?"
Casey snarled. "Doesn't matter what it's called. We have to find it quickly."
"Ok. What do we know about its whereabouts?"
"Flown into LAX this morning but wasn't stopped in time," Sarah told him. "It does transmit a signal, though, but very weak."
"So, if I can detect this signal, we can find it. Right?" Chuck asked.
Casey looked at him for a few moments. "Seems your skills might be needed."
"Is that over in your swanky new base?"
"Yeah." Casey looked around the near-empty store. "Now looks like a good time."
Sarah stood next to Casey, several feet behind Chuck. They were watching him at the terminal. She couldn't help smiling.
"Watching your boy toy having fun?" Casey asked.
"He's like a kid in a candy store. So much technology, and now, being able to use it makes him very happy." She looked at her partner, and her smile grew larger. "It is a bit contagious."
He nodded. "I feel the same when I walk in that armory knowing I will be able to play with some of those toys."
She laughed as she felt his excitement.
She looked back at what Chuck was doing. "Those aren't his IT skills or the Intersect, Casey. He is just like a field analyst."
"Yeah. I am trying to get the general to see him that way," Casey replied.
Sarah could read his thoughts about how that was going but had to ask. "How's that going."
"I think she agrees, but Graham is dead against it." He looked at his partner. "I don't think she wants to seem weak when he's with her."
She could understand that.
"Found it!" Chuck called out.
The two agents walked over to him.
Sarah thought at Chuck. 'Well done, my love.'
'Thank you,' he replied.
"How'd you do it?" Casey asked. They had been completely unsuccessful before.
"I filtered out all the noise from all other types of devices, and there it was," Chuck replied.
Sarah knew from reading his mind that it wasn't that simple but also knew Chuck didn't like to boast.
Casey made a call to get the reinforcements they wanted.
Sarah stayed by Chuck. "You can monitor us from here, Chuck," she told him.
Chuck didn't really want to go out on the mission, so was happy to stay behind. 'Take care, Sarah. I don't want to lose you.'
'I always take care,' she replied.
"They'll be there in half an hour," Casey said as he ended the call.
She looked at him. He looked happier than she'd seen him in a while. She grinned. "Showtime!"
The huge black guy had escaped after punching Casey on the left side of his face and leaving a scar from his ring. The fact that Casey had flown across the room from that punch was not lost on any of the participants.
However, Casey had managed to secure The Cypher.
The two agents were now back in Castle and facing the large monitor and the two leaders for the debriefing. Chuck sat at the back of the room and listened in.
"Excellent work. Sarah. Casey," Graham said. "A transport will be taking The Cypher out of Los Angeles."
As it seemed to be an NSA device, Sarah looked at Beckman. "General, what exactly is the Cypher? I mean, mercenaries break into the NSA lab, and it's the only thing they take?"
Beckman replied, "The Cypher is the artificial brain for the new Intersect computer."
That got everyone's attention. "The new Intersect?" Chuck asked. He wasn't supposed to know about this.
Graham replied, "We've been working on a new one ever since the original Intersect was destroyed. The Cypher is the final piece."
Chuck knew all this but had to ask, just to see what would be said. "Uh, wait, time out just for a second here. What- what happens to me, the old Intersect?"
Graham didn't bat an eyelid. "Tomorrow, the new computer will be online, and Operation Bartowski officially comes to an end. You'll be done with us. No more briefings, no more missions, no more spies." Chuck did think that sounded good. Well, apart from one particular spy. Graham then said, "Enjoy the rest of your life, Chuck."
Beckman leaned forward and ended the call.
'Bastard!' Chuck thought.
'He really is a bastard!' Sarah agreed. Both knew Graham meant the next two days with that last comment.
Sarah followed the two men into the car park from the yogurt store. She had to ask Casey if he had heard anything from the general or Graham. "Not yet," he replied. "But I'm expecting it. Get ready to leave."
"Give me the nod when you get the call," she replied.
She wandered back into the store. She had everything packed in her car in case this happened. That included what she had packed for Chuck, other than what was in secure storage.
As she got into the store, a call came through on her phone.
She looked at who it was from. Graham.
"Director," she answered.
"Sarah, I will have a new assignment for you next week. You can have the rest of this week off, but you should collect the assignment details from someone flying into LAX tomorrow evening at around 7:30."
"Can't they leave it somewhere secure?" she asked.
"It's too sensitive," he replied.
She knew this was a deliberate ploy to get her away from Chuck, but she had to accept it.
Half an hour later, Casey walked over, saying, "I left something down in Castle." She looked up at him. He nodded at her.
It all fit. Tomorrow they would put their plan into action.
That morning, Ellie and Devon had told them they would be working evening shifts. "Lots of people off sick at the moment," Ellie said.
"No problem," Chuck had replied.
Chuck now felt sad as they probably wouldn't get to spend any time with the older couple before they left. For good.
The two of them headed into the bedroom straight after eating dinner. Chuck contacted his father.
"What happened to the Intersect?" Chuck immediately asked as Stephen appeared on the monitor.
"The NSA scientists hadn't been involved in the testing, and it was sent to them," Stephen replied. "Fulcrum must have found out."
"It's being sent over here to LA for some reason," Sarah mentioned.
"I didn't know that," Stephen said. He obviously thought for a few seconds. "I think they must have people in LA to alter the code."
That sounded worrying. "Could they change what you have done?" Sarah asked.
"I doubt they have anyone that good," Stephen replied. He looked at them. "I think my old 'friend,' Ted Roark, might be involved." The two could almost hear the quotes around the word friend.
Chuck responded. "He has the best tech team in the US."
"Unless they have been working on a replacement Intersect, then they won't have time to do that now," Stephen told them.
"We intercepted it but don't know if it has been tampered with," Chuck said.
"We'll find out when it is activated, I guess," Stephen said.
"That's tomorrow night," Sarah stated. Stephen looked at them. His worry was evident. "We will be going into hiding," she told him.
"I will connect up so that we can talk securely," Chuck reassured his father.
Stephen nodded but still looked worried. "Good luck."
Straight after the call, Chuck and Sarah undressed each other and made love in their bed. After all, it might be the last time they ever spent time in this bed. A bed with many fond memories.
The following day, what they now thought of as D-Day, Sarah and Chuck got up slowly and had no intention of going in to work. Ellie and Devon had returned and gotten a small amount of sleep before they had to go back to the hospital.
After lunch, the two of them heard a disturbance outside. "That sounds like Casey's place!" Chuck said.
They went to look and saw Casey's door open. That certainly wasn't normal. They rushed over and found Casey's face covered in white powder. He was gasping for breath and obviously struggling.
Sarah turned to Chuck. "Do Ellie or Devon have adrenaline?"
"Not in the apartment," he replied.
"Regan," Casey just about managed to say.
Sarah leapt up and grabbed the Regan photo, and turned back to Casey, who was now unable to move, just staring at the prone man.
'Get out of here, Chuck.'
'Why?' he asked.
'Because you won't want to see this. Go!' She imagined holding a syringe above Casey.
He got out of there quickly. She smashed the picture and found the syringe, which she grabbed and plunged the needle into Casey's heart.
"Come on, Casey!" she cried out. She rushed to the kitchen and filled a bowl with water, and threw it on Casey to wash the powder away.
Casey grabbed her wrist. "Took the cypher. They may come for you two."
Sarah panicked. She had sent Chuck out. She rushed over to the other apartment. She was so relieved to find him in the bedroom on his laptop. "Thank god you are ok!" she cried.
"I read his mind about The Cypher before I left."
Sarah hadn't thought of doing that because she was so focused on saving Casey's life. She looked at the screen. Chuck was tracking The Cypher. which was on the move.
Sarah called Graham and got no reply, so she called Beckman, who sounded surprised. Sarah started talking immediately, "Whoever came to collect the cypher wasn't NSA. They nearly killed Casey. Chuck and I found him, and Chuck has tracked down The Cypher. It's not left LA yet."
"You have to get it back. What do you need?"
"NSA or CIA people we can trust. Some at the apartment block and some to go after The Cypher when we know where it ends up.""
Beckman replied, "I'll get that arranged and send contact details to you for the second team. When you know where to go, tell them."
"Send it to Chuck. I'm going back to Casey to make sure he recovers."
Beckman paused for a second before saying, "Will do."
Sarah ran back over to Casey. He was now looking better but was in no state to go on the retrieval mission. She helped him up and over to Chuck.
Casey was rapidly recovering.
After a few minutes, Chuck said the signal had stopped moving. He zoomed in on the location and told them where it was. This was timely, as he received a text from Beckman with a number, so he called it and told the man who answered where to go.
Sarah grabbed his phone off him. "This is Agent Walker. I'll meet you there in twenty minutes."
Casey stood. "I'm coming too."
She looked at him. "You'd be no help. Stay and protect Chuck until backup arrives."
She grabbed her keys and was going to run out when Chuck called to her. "I'm coming too."
She turned back. "No. You're not. You have to look after Casey." 'Please!' she added, before she ran out.
Sarah couldn't believe how this had happened. She'd gotten separated from the dozen marines and was now facing the huge black man they had seen before. He had disarmed her, and it was now a standoff between them. She could hear gunfire from the floor below.
For such a large man, he was fast, but she was faster, and being able to read his moves before he made them helped too. However, he still managed to hit her a couple of times. Each blow sent her flying as there was so much power put in.
When she aimed to kick his face, he went to grab her ankle, and she read that move. She kicked his face with the other foot, sending him to the ground.
He got up and tried to grab her. That wouldn't be good, as he would probably be able to crush her. She dropped, and his arms closed on themselves. She kicked his feet out, and as he dropped, she kicked him in the balls. That got him groaning and slow to rise.
She rushed over and grabbed her gun from the floor. When she turned, he was just getting up. She shot him in his left knee. He tumbled to the ground. Just at that point, Casey rushed in, looking much better than before. He quickly rushed to the man and got cuffs on him.
Chuck followed Casey in and saw Sarah looking bloodied. He was going to rush to her, but she said, "The Cypher." She looked over to the case that contained it. She had read that on the large man's mind. Colt, one of the other men had called him. 'The Cypher is in that case, Chuck. Go and get it.'
Chuck soon held The Cypher up to show the other two. He then helped Sarah off the floor. 'We'll talk about staying safe when we get home,' she told him.
'Casey made me bring him,' Chuck replied. 'We were both worried about you.'
It was now nearing 7pm, and it was time for Sarah to head to the airport. Casey knew the plan and disabled all the surveillance early. He was going to have to do this for the planned execution anyway.
Sarah and Chuck set off.
When they arrived at the airport, it was 7:25. She quickly headed to arrivals.
The courier arrived, and after the required codes were exchanged, she received a large envelope, which she took with her.
When she got to her car, she dropped the envelope on Chuck's lap and set off. In no time, they were on the 405 heading away from LA.
Chuck had left his watch at home, and they both switched off their phones. The burner Chuck had grabbed for them was switched on, though.
"I wish I could've told Ellie about going away," Chuck said.
Sarah replied sadly, "The less she knows, the better, Chuck. For our safety and hers."
At 8:10, a call came through on the phone. Only Casey had this number on the burner Chuck had given him. Sarah frowned. This was not planned.
Chuck put it on speaker. "Casey, I wasn't expecting to use these for some time," Sarah said. They had agreed to keep silent unless something drastic happened.
"The new Intersect has been destroyed," Casey told them.
"What?!" both in the car shouted.
"The Cypher must have been a Trojan horse, a sabotage device. The moment it came online, it exploded."
"Taking the agents with it?" Sarah asked.
"Yeah. Six agents," Casey paused, then added, "Graham too."
Sarah gasped. She no longer had any trust in the man and only negative feelings, but he had been part of her life for eleven years.
Chuck took hold of her hand. She looked at him and could see the sympathy even before his mind soothed hers.
"You're still the only Intersect, Chuck. Beckman is asking for you."
"Oh, so now I can live?" Chuck sarcastically replied.
"She told me she was glad it had worked out this way. She didn't agree with Graham and wanted to keep the team together. Seems now she can."
Sarah guided the car off the freeway. They were heading home.
"She has finally agreed that you should become an Analyst," Casey added.
Sarah's eyes lit up. Chuck read her mind. That meant there was no reason for them to continue to hide their relationship from the general.
When the call ended, Chuck said, "Dad will be pissed. All that work he put in wasn't needed."
"I think he will just be glad you are safe, Chuck," she replied.
As they headed back to Echo Park, both were now thinking of a very different future.
Chuck was overjoyed that he would be able to still see Ellie, Devon and Morgan. Of course, he would still be in danger because of the Intersect and Fulcrum, but he would still have the two best agents protecting him. One of those being the love of his life, who wouldn't now be sent away.
He looked down at the envelope on his lap. "Shall I open this?"
"Might be fun to see where he would have sent me," she replied. "But it will probably be a recording for me to watch. I expect it to be the other side of the world and, knowing him, an assassination of some sort. Maybe a series of them."
He left it where it was. Both shared the same thought. Neither wanted to be apart, and now they could be together without looking over their shoulders all the time. "Love you," they both said at the same time.
A.N: So, safe and sound. Well, they still have all the fun of season 2 to go yet!
{lease let me know what you thought of this chapter, other than too short, that is!