Make a Wish

A/N: Chuck Verses Tom Sawyer was one of my favorite episodes. What if Chuck stopping Morimoto's weapons satellite served as the turning point for his spy life, and his relationship with Sarah?

The story will begin at the conclusion of Tom Sawyer in a modified canon setting.

This story was inspired by another story, "What Would You Like?" by stars90. I enjoyed the concept presented by stars90, and it seems my brain can't get away from it. So, I'm taking a gamble and letting the inspiration from "What Would You Like" guide me.

I would like to thank stars90 for graciously allowing me to use the concept from "What Would You Like" in my story. If you haven't read "What Would You Like," I highly recommend it. You can find it in my Favorites. Our stories will have similarities, but I did make a conscious effort to ensure "Make a "Wish" has it's own unique flavor. Plus, I have a storyline planned well beyond Tom Sawyer.

One major difference I will point out is the attitude of the higher ups in how they deal with Chuck, especially Beckman. You'll just have to read each of our stories to find out the differences.

I balanced the mix of narrative and dialogue as much as possible.

There will be some strong language, but I kept the romance scenes tame.

As for Chuck and Sarah, I focused on relationship development. I believe things would have gone a lot different in canon had they gotten together early. I do strive to keep the characters in character. I will try to bring all the elements from the show together as much as possible. There will be drama, humor, and action.

Thoughts and phone conversations are in italics. My apologies in advance if you see a mistake, grammatical or technical. I do proofread each chapter before posting, but none of us are perfect.

I do hope the reader finds the story enjoyable. I will update as often as I can.

Disclaimer: I don't own Chuck. WHAAAA!

Chapter 1: Star Wars

Brigadier General Diane Beckman was sweating bullets. The Commanding General of NORAD had just informed her an ICBM was fueled and ready for launch. Beckman was video conferencing NORAD, Major Casey, and the Launch Control Center at Vandenberg, Air Force Base in preparation for the launch.

The target: A nuclear weapon's satellite activated by a terrorist. The satellite was targeting the West Coast of the United States.

The young Air Force Captain manning the Launch Control Center at Vandenberg addressed Major Casey. "All safeties are off, missile is fueled and ready. Missile is armed. You now have control of the missile, Major Casey."

Casey popped his knuckles and lifted the safety on the portable missile control console in Castle. I never thought I would ever have to fire a nuke.

Suddenly, a radar technician monitoring the weapons satellite broke the momentum of the firing sequence.

"General Greer! Something's happening with the satellite! Wait a minute… Sir! The satellite just disarmed! All weapons are on safe! She's bugging out, General, and heading back to high orbit!"

General Greer ran over to the radar console. "Are you sure, Lieutenant?"

"I've never been more certain of anything in my life, General. The satellite is standing down, Sir."

Greer shook his head in relief. "Dear God…that was close!"

Casey's phone rang at that instant. "Walker?"

Silence filled the air as everyone focused their attention on Casey. Casey replied, "Understood," then hung up his phone.

"General Beckman, Walker has control of the TV station. Bulsara and his team are neutralized."

Beckman took a deep breath and muttered, "Thank, God." She composed herself and addressed Casey.

"Major Casey, how did Agent Walker obtain the code?"

Casey replied professionally. "She didn't, General. The Intersect obtained the code."

Beckman quickly addressed Greer and the Space and Missile Operations Officer at Vandenberg. "Gentleman, I appreciate your assistance with this matter. I need to debrief Major Casey. General Greer, I'll be in touch."

Before anyone could reply, Beckman disconnected the feeds from NORAD and Vandenberg.

"Alright, Major. We're secure."

Casey shook his head. "You're not gonna believe this, General. Bartowski found the code playing Missile Command. His theory about Morimoto hiding the code in the game was correct. Bartowski relayed the code to Walker after she took out Bulsara's team. Walker is waiting for a cleaner team to arrive at the TV station."

Beckman's eyes bugged out of her head. "I'll be damned…Bartowski made it to the kill screen?"

Casey furrowed his brow. "How did you know about the kill screen, General?"

Beckman waved a hand. "Never mind. Where is Mr. Bartowski at the moment, Major Casey?"

Casey glanced over at one of the video feeds. "Ma'am, Bartowski is currently being carried around the Buy More like some nerd god."

Beckman cut Casey off. "That'll do, Major. I didn't ask for specifics. Alright, retrieve Mr. Bartowski and recall Agent Walker once her backup secures the TV station. There will be a briefing in one hour."

Beckman disconnected the feed. Casey shook his head. "The moron saved the entire West Coast using a damn video game. This assignment gets more and more bizarre by the minute."

White Housing Briefing Room

President Zachary Levy couldn't believe his ears.

"You mean to tell me this young man has our entire intelligence database in his head? Why in the hell wasn't I informed of this before some terrorist whack-job decided to hijack a nuclear weapons satellite?"

CIA Director Tom Hardy maintained his composure during the dressing down from the President.

"Mr. President, the fewer people who knows about Operation Bartowski, the better. We kept you out of the loop for operational security."

President Levy leaned forward. "Director Hardy, the last time I checked, I am the President of the United States. Don't give me that plausible deniability crap. I know all about Fulcrum and the complications associated with making this clandestine war at home known to the general public. My problem, Director, is this man is an American citizen. Ever heard of that little document called the Bill of Rights?"

Director Hardy frowned. "Mr. President, the Intersect is an intelligence asset. There are protocols we must follow to maintain operational security. If this man fell into the wrong hands, it could spell disaster for this country."

President Levy had an incredulous look on his face. "Is that what you're calling him? The Intersect? Does this young man not have a name?"

Director Hardy turned his head slightly to ease his tension. "As I mentioned, there are protocols we must follow…"

President Levy had had enough. He leaned forward and pointed at Director Hardy. "Stop right there, Director Hardy. This man has a name, and he will be addressed by his name."

Director Hardy chimed in. "He's an intelligence asset, Mr. President."

President Levy slammed his fist on the table. "He's an American citizen!"

The room grew quiet as everyone froze at the President's wrath.

The President glanced away in frustration. "Ladies and gentlemen, no matter which way you all try to spin this to me, the situation with Charles Bartowski is just plain wrong. This man is an American citizen. Every one of us in this room has an obligation to protect the citizens of this great nation, and our way of life."

President Levy paused. "Director Hardy, how did Mr. Bartowski end up with the Intersect in his head?"

Director Hardy opened a folder in front of him. "Mr. President, a year ago, one of our agents stole the Intersect and emailed it to Mr. Bartowski."

President Levy's jaws dropped. "Wait…you mean to tell me a federal agent emailed our secrets to a civilian? Do they know each other?"

Director Hardy nodded. "Yes, Mr. President. Agent Bryce Larkin and Mr. Bartowski were roommates in college."

President Levy flipped a few pages in the dossier of Chuck in front of him. "Wait a minute, it says here Agent Larkin had Mr. Bartowski expelled from Stanford on trumped-up charges of cheating. What the heck did Mr. Bartowski do to Agent Larkin, steal his girl or something?"

Director Hardy winced. "Uh, actually Mr. President, Agent Larkin stole Mr. Bartowski's girlfriend."

President Levy blanched. "You're kidding! What a douche-bag!"

The Chairman of the Joint Chiefs, General Marcus, snorted.

Director Hardy closed his eyes to gain his composure. "Mr. President, what is it that you want us to do? Mr. Bartowski is the most important intelligence asset in the world. If he falls into the wrong hands and is tortured, it would compromise our intelligence capabilities."

President Levy leaned back in his chair and pondered Director Hardy's words. "I see our dilemma, Director. Where do we draw the line on taking away the rights of citizens in the interest of national security, while protecting those citizens from harm?"

Everyone in the room glanced around at one another, not sure how to respond.

President Levy leaned forward. "I'll tell you where we draw the line. I can understand the need for intelligence assets, but most of these people are criminals, or enemies of the state themselves. Mr. Bartowski is an American citizen caught up in a God-awful mess he neither volunteered for, nor was asked to be a part of. It seems to me we created this mess. We didn't protect the Intersect computer properly and it was compromised. We can't punish this young man for our sins. In fact, from what I've read in the reports, his conduct in this operation has been exemplary, and he has given his full cooperation. It seems to me Charles Irving Bartowski is not an asset. He is one of this nation's brave sons, who although didn't volunteer for duty, answered when duty called him."

President Levy thumbed through the mission reports on his desk and retrieved one particular report that caught his eye. "I would like to read an excerpt from one of Agent Walker's reports."

The President glanced down and began reading. "Mr. Bartowski has exhibited no hostility or lack of cooperation with either myself or Major Casey. He gives his complete cooperation, time, and talents to this team, and risks his life on a day-to-day basis with little or no recognition for his efforts. Even if Mr. Bartowski were to be recognized, the humbleness in him wouldn't accept any other explanation for his actions other than his desire to do the right thing. He has been instrumental in the thwarting of numerous criminal or terrorist operations with no training. Mr. Bartowski has placed himself in jeopardy on numerous occasions, notably saving the lives of myself and Major Casey. He has remarkable analytical and problem-solving skills. Although he hosts the Intersect, he is able to analyze the data presented by the Intersect, disseminating said information into actionable intelligence in a matter of seconds."

President Levy laid the paper down and took a breath. "This young man was abandoned by his parents and raised by his sister. He was denied the opportunity for a successful career by his college roommate, who also happened to be responsible for his involuntary induction into the intelligence community. And now, he is denied the basic privilege of living a normal life because he is considered an intelligence asset. Folks, this man can't even pursue a real relationship because of our mandate he and Agent Walker act as a couple as part of Agent Walker's cover."

The President turned his attention to Director Hardy. "Director Hardy, has he asked for anything?"

Director Hardy shook his head. "No, Mr. President. But, I do have a request to General Beckman via Agent Walker to award Mr. Bartowski his Stanford degree for his service. Beckman approved the request this morning. Agent Walker will be informing Mr. Bartowski about the degree this evening."

President Levy nodded. "Good. Awarding Mr. Bartowski his degree will only be the beginning."

Director Hardy looked confused. "What do you mean, Mr. President?"

The President had a look of determination on his face. "I support the need to protect Mr. Bartowski, and I'm on board with that. But, it is time to make some serious changes in how we treat him. I'm not happy with the fact we are using the steel-toed approach when there is no need for it. It seems to me Mr. Bartowski is a partner in all this, rather than an asset. He will be treated as such. I want this young man paid for his services. If he is acting in the role of an analyst, he will be paid as such."

The President closed the folder. "This operation will remain under the oversight of the Joint Chiefs of Staff. The inter-agency rivalry between the CIA and NSA has already proven costly, namely our secrets in the head of a civilian."

Director Hardy sighed. "Mr. President, the CIA and NSA has invested millions in this project."

President Levy held up a hand. "I understand that, Director Hardy. The CIA and NSA will still be able to use Mr. Bartowski for operations. But, you will use him as an employee."

Director Hardy nodded. "Yes, Mr. President."

President Levy held up a finger. "There's one more thing. I read in the reports there was a termination order placed on Mr. Bartowski when the Beta Intersect was tested a few months ago. I want to make it plain and clear when I say this. If I hear of another, you and Beckman will spend the rest of your natural lives in Fort Leavenworth. Is that understood, Director?"

Director Hardy's eyes widened. "Understood, Mr. President."

President Levy checked his watch. "Good. Get Beckman on the line. I'll take the call in the Oval Office."

Director Hardy blinked. "General Beckman should be finished briefing the team by now."

Without another word, the President got up and left the room. Director Hardy flung his pen on the table in frustration.

Echo Park, 7:15PM

Chuck entered his apartment and was immediately hugged by Ellie.

"Chuck! I'm so proud of you!"

Chuck smiled. "It's just a video game, El. Although I am the best Missile Commander in the world." And stopped an actual missile...

"Chuck, I'm not talking about some stupid video game, I'm talking about this!"

Ellie handed Chuck a small box. "Sarah told us what's inside."

Chuck gave his sister a questioning look, then opened the box and removed a portfolio with the Stanford logo stamped on the cover. Chuck quickly opened the portfolio and his eyes widened.

"My diploma?"

Ellie clapped her hands in excitement. "Well, don't act so surprised."

Devon chimed in. "You sly dog! Sarah also told us what you've been doing behind our backs."

Chuck looked astonished. "She did? Really?"

Devon turned serious. "Yeah. No wonder you've been such a mess this past year."

Chuck's eyes widened. Sarah told Ellie and Devon about the Intersect? No way!

Ellie smiled. "Why didn't you tell us you were taking online courses?"

Chuck laughed nervously. "Oh! Oh, right! That…"

Devon broke Chuck's stammering by handing him two beers. "Sarah's out on the back porch. You two have some celebrating to do. You'll thank me for that ginseng shake in the morning." Devon winked after the last remark.

Ellie rolled her eyes, but smiled at her little brother. "You really surprised me, Charles."

Chuck gave his sister a solemn smile, thinking the degree wasn't real. Ellie and Devon left the room, while Chuck made his way to the back porch.

Sarah was staring off in the distance, but turned, giving Chuck a small smile.

Chuck took a breath, trying to mask his disappointment. "Thanks for the fake diploma."

Sarah quickly responded. "What do you mean?"

Chuck shrugged. "I get it. You know, you had one of your CIA pals doctor it up to get Ellie off my back."

Sarah shook her head slowly. "It's real, Chuck."

Chuck furrowed his brows. "Come on."

Sarah shrugged. "I'm serious. You graduated."

Chuck looked confused. "What about my last 12 credits?"

Sarah took the beer offered by Chuck and gave him an appreciative smile. "Casey and I felt your exceptional field service ought to count for something, and Stanford agreed."

Chuck opened his beer, injecting levity in his tone. "Huh. You mean by exceptional, you mean, uh, I don't know, like decrypting weapons satellite codes?"

Sarah smiled at the banter. "Electrical engineering?"

Chuck grinned. "Or, running from exploding games of Missile Command?"

Sarah didn't miss a beat. "Physical education?"

Chuck smiled warmly at Sarah.

Sarah spoke in earnest, and reached out to touch Chuck's beer with her own in toast. "You earned it, Chuck."

A moment of comfortable silence passed between the two. Chuck replied in warm conviction. "Thank you."

Sarah smiled, then turned and pointed to the sky.

"See that star out there over the horizon? That's the Air Force bouncing Morimoto's satellite off the atmosphere and burning it up."

Chuck stared at the satellite, pondering the day's events.

Sarah turned and said in a soft tone. "Make a wish. It's yours."

Chuck stared off into the distance as his emotions started boiling to the surface. He didn't want to cry, but he couldn't help it. The piece of paper in his hands represented many things to him. Mostly, the chance at a real life.

A chance that seemed so far out of reach.

Chuck blinked away his tears. He spoke in a broken tone. "I appreciate this more than you know, Sarah."

Sarah turned and noticed Chuck struggling. A look of concern adorned her face as she touched his arm.

Sarah spoke softly. "Are you alright?"

Chuck sat his beer on the rail and reached over to place his hand on top of Sarah's. "I was thinking…I'm upset with myself for making so many bad choices after Stanford. I need to start taking better control of my life and stop looking for excuses for my own mistakes."

Sarah squeezed Chuck's arm in comfort. Chuck took a breath and continued.

"Sarah, what good is this degree if I can't even use it? I mean, what if I never get rid of this…thing out of my head?"

Chuck turned and met Sarah's eyes. Sarah's heart broke seeing the sad and lost look in Chuck's face.

"We will figure something out. I promise."

Chuck wiped his face quickly and took a breath. "Sarah…something has been bothering me, and I hope this isn't awkward, but I need to know if something is true that Bryce told me his last visit."

Sarah released her hand on Chuck's arm and leaned on the rail, studying Chuck closely. Bryce…what did you do?

Sarah softly replied. "Talk to me, Chuck. What did Bryce say?"

A look of anguish appeared on Chuck's face. "I'll, uh, I'll get to Bryce in a minute. But first...I said something to you that night by the fountain after the Von Hayes mission…and I wish I could take it back. I didn't mean it the way it came out, and...I can't get it out of my head, Sarah. I made a mistake."

Chuck turned and faced Sarah. Chuck's eyes met Sarah's and he spoke straight from the heart. "That night…when I told you we could never be together because you weren't normal…I didn't mean it like that."

Sarah cast her gaze downward to school her emotions. She took a breath and stared in Chuck's eyes. "Chuck, I know I'm not normal."

Chuck shook his head. "Please, let me explain. What I meant to say was, you're beyond normal, Sarah. You are the most amazing woman I have ever met."

Sarah smiled softly and glanced away. Chuck continued. "I did mean what I said about you being the best thing that has ever happened to me. I don't know what I would do without you."

Sarah reached out and intertwined her hand with Chuck's, not daring to make eye contact.

Chuck looked down at their hands and smiled. "My point is…I'm sorry about the way I handled that conversation…and I regret what I said about you and I never being together."

Sarah quickly raised her eyes. Chuck held up a hand and smiled sadly. "Don't misunderstand me. I'm not nagging you again about us, I promise. I know you have a job to do...I see that now. I'm not asking for anything. But…now for what Bryce said."

Sarah nodded, and spoke softly. "It's okay, Chuck. You can tell me."

Chuck gulped loudly. "Bryce told me…our feelings for one another would get us killed…Sarah is that true?" Chuck's eyes bore into Sarah's.

Sarah stared in Chuck's eyes lost for a moment until his words clicked. She glanced away and released Chuck's hand, turned, and started pacing. Chuck immediately panicked.

"Sarah…Sarah please don't be mad at me if I crossed a line…"

Sarah turned on Chuck. "That's why you broke up with me? Because of Bryce…" Sarah turned away and her mouth widened. Sarah muttered, "Sonofabitch!"

Chuck stared at his feet, thinking Sarah was about to lay into him for overstepping his bounds.

Sarah began ranting. "I knew I should have talked to you about Bryce's intentions! Bryce spent that entire mission trying to seduce me and rub our past relationship in your face. He kept lecturing me about my feelings for you…and now I see I wasn't the only one that arrogant piece of shit was lecturing to…that conniving bastard!"

Chuck suddenly raised his eyes, stunned. He had never seen Sarah this angry.

Sarah continued her rant. "Just when things were going so well for us, Bryce shows up and ruins everything I worked for! I even went to your apartment to make sure you were okay the night you came to my hotel and found Bryce there…" Sarah trailed, remembering the night Bryce Larkin once again drove a wedge between her and Chuck.

Sarah never forgot the look of dejection on Chuck's face when he tried to romance her with the "Montgomery," only to find Bryce in her hotel room. Bryce had arrived mere seconds before Chuck. Sarah hoped her arrival at Chuck's apartment later that evening after making certain Bryce stayed elsewhere, made things right.

The simple candlelight dinner in the courtyard of Echo Park with Chuck that evening was one of Sarah's fondest memories.

Sarah took a breath. "It's hard enough for me to hide behind the cover, but just when I feel I could finally open up to you, you tell me we can't be together because BRYCE convinced you my feelings for you could get me killed? I'm a spy, Chuck! You should have let me decide what I can and can't handle!"

Sarah paced back and forth angrily. Chuck stared at his feet as tears streamed down his face.

Sarah suddenly paused and turned to face Chuck. She noticed him fighting to keep from breaking down.

Then, it dawned on Sarah. Chuck broke up with me thinking he was protecting me. How can he be so sweet, yet so foolish?

Sarah walked over and gently took Chuck in her arms. Chuck said in a broken voice, "I'm sorry, Sarah. I never meant to hurt you."

Sarah took a breath. "I know, Chuck. You thought you were protecting me. You really need to stop listening to Bryce, and start trusting me. Do you understand?" Things have gotten too complicated. I'm tired of this. It is time I told Chuck how I really feel...what I wanted to tell him that night.

Chuck nodded. "I do trust you, Sarah. I'm sorry, I should have talked to you. But when you got hurt during the Von Hayes mission...I...I almost lost it seeing you lying there so lifeless. That's why I listened to Bryce. I couldn't live with myself if anything happened to you because of me."

Sarah tightened her embrace and her breath hitched. She closed her eyes and took a calming breath. Oh Chuck... "No one has ever cared about me the way you do...but you should have talked to me about this. Chuck, what got me injured was Bryce delaying me when you were taken by that Fulcrum agent. He wanted me to abandon you and pursue Von Hayes. That's why I got hurt."

Chuck opened his eyes. "Really?"

Sarah sighed. "Really. Chuck, I got hurt because of Bryce, it had nothing to do with my feelings for you. Here's the feelings for you saved your life, that's why I ignored Bryce and came after you. Had I arrived sooner, that Fulcrum agent never would have made it to her getaway car, and I probably wouldn't have gotten hurt. More could have been killed."

Sarah's words finally clicked. Chuck broke the embrace and placed his hands gently on Sarah's arms.

"Wait...your feelings for me...Sarah, what does that mean? And, and…the things you said about us, the cover, and you opening up to me…Sarah…"

Sarah was about to respond when her phone buzzed. Dammit!

Sarah held up a finger and let her eyes calm Chuck. Sarah retrieved her phone and held it up for Chuck to see. Chuck nodded and backed away. Sarah reached out and grabbed Chuck's hand, shaking her head. Sarah held Chuck's hand tight as she answered the phone.

"What is it, Casey?"

"Walker, are you still at Bartowski's?"

"Yes. Is something wrong?"

Casey spoke quickly. "Beckman needs us all in Castle ASAP. I'm not sure what's going on, but it sounded urgent."

Sarah stared at Chuck in concern. "Okay. We're on our way."

Sarah hung up the phone and huffed in frustration. Chuck looked concerned.

"Sarah, what's going on? Another mission?"

Sarah nodded. "I think so. Casey said it was urgent. Whatever it is, it's something big. We need to get to Castle immediately."

Chuck looked confused. "What could possibly be bigger than stopping Freddie Mercury from starting World War III?"

Sarah raised an eyebrow in confusion. "Freddie Mercury?"

Chuck tried to explain. "Farrokh Bulsara, you know, Freddie Mercury...Queen? Oh, never mind. I'll, uh, tell Ellie we decided to go out."

Sarah grabbed Chuck's arm gently. "Chuck, this conversation isn't over."

Chuck asked nervously. "Concerning...Freddie Mercury?"

Sarah put her hands on her hips. "Seriously?"

Chuck stared at his feet, muttering "Oh."

Sarah grabbed his face and met his eyes with her own. "You're not in trouble. Thank you for telling me the truth about what happened."

Sarah smiled and released Chuck's face. "Now, go tell Ellie we're going out to celebrate your graduation."

Chuck sighed. "Yeah…it'll be good for the cover." Chuck's eyes widened. Did I just say that out loud?

Sarah closed her eyes and took a breath. "Chuck…after we deal with Beckman, what you and I need to discuss has nothing to do with the cover."

Chuck studied Sarah carefully. Sarah allowed her eyes to do the talking for her. Chuck glanced at his feet and nodded, giving Sarah a warm smile before turning to walk to Ellie's room.

Chuck made it into the living room while Sarah headed for the door. She turned quickly. "Oh, one more thing."

Chuck turned. "Yeah?"

Sarah stared at Chuck through her eyelashes. "Tell Ellie not to wait up. After this briefing, we have a lot to talk about."

Chuck's eyes widened. Sarah gave a coy smile and quickly left the apartment. Chuck gulped loudly.

"Don't freak out."

A/N: The spelling of Zachary Levi's last name was changed on purpose, ie, "Levi" to "Levy."

The final scene from Tom Sawyer is one of my favorites from the series, and I didn't want to change a thing about it from canon. I did expand it to add a few more goodies to the storyline, and set the stage for things to come. There is also a conversation about the break-up in "What Would You Like." I added that in as a tribute.

Beckman implied the Joint Chiefs had a major role in providing oversight for Operation Bartowski in the series, so I attempted to clarify that in the President's mandate for operational oversight of the project. There are several little goofs or plot holes from the series I plan to tackle as the story progresses.

I do hope I was not too far off the mark with the missile scene at the beginning for my Air Force friends reading this.

Next chapter, things get a little tense, but I have a few surprises in store...stay tuned.