Summary: Chuck was never kicked out of Stanford. In fact, he and his Roommate/Best Friend Bryce Larkin have joined the CIA together and went straight to Project Omaha where they meet a third member for their team: Daniel Shaw. Here, the three of them became Insterects and have become an unstoppable team on missions. Until five years later (2007), Shaw betrays his team, going AWOL on a mission, leaving Chuck and Bryce stranded in Colombia.

Prologue

CIA HQ Langley

July 14th, 2007

"Agents Walker, Rizzo, Miller, come sit." The baritone voice of the Director of the CIA Langston Graham said with no preamble as he entered his office.

Sarah Walker, the unofficial team leader of her Squad led her members to the seats across from Director Graham's desk and sat down first followed by her team. The C.A.T. (Clandestine Attack Team) Squad knew better than to ask questions first as the Director sat down behind his desk, pulled out a few manilla folders all labeled TOP SECRET on them and placed them on top of his desk.

"Before we start," He started, looking up at the three women across from him, "What do you know of a project called Omaha?" Graham looked closely from his seat to see their reactions, of which there was none. He was pleased to see they stayed silent as well, not even asking a curious question. "Alright then, the beginning it is. Open the files. All of you have the clearance for this."

The women side-glanced at each other for a second before each going to grab one of the TOP SECRET folders.

They each opened their own file, and inside was an information dossier about their fellow agents. Sarah's file had a picture of a tall, lanky-looking athletically built curly haired man with a soft smile and brown eyes. Alongside it, was a name and the main alias he goes under:

Charles Irving "Chuck" Bartowski

Charles Carmichael

Then she read the record of all the amazing things he has done with his two partners, James T. Anderson, and Clark Olsen. There were about thirty pages of accomplished mission after mission (most of it redacted of course). One thing that really stood out after her (rather quick) read through, was that this Agent had never killed anyone in these missions. From he she had seen, he disables and tranqs his combatants. She finds herself a little jealous of this fact. How can someone like this Agent Bartowski be a Spy and not having killed anyone? Hasn't he even had a Red Test?

She glanced through his Dossier again, to find that no, Agent Bartowski never had a Red Test. He was put in this Project Omaha thing during his Senior year at College in Stanford, where he also completed his Computer Engineering Degree and Masters. Then he was sent to the Farm with his two partners, and they had top marks. Not quite up there with her, but they were all really good. Though she noted that Agent Bartowski had some issues with the Seduction Course of the Farm. Inwardly, she arched an eyebrow at this, outwardly, her face remained unconcerned as she read on.

As she read about the parts she could read, Sarah saw that Agent Bartowski has a Sister living in Burbank, California. She saw the phone records as well, even when he was on a mission. She noted that these also lasted just under a minute, not even long enough to get a trace if someone was looking for him.

So, he cares about his family. Sarah thought, thinking of her own mother, one that she had to cut ties from after her last solo mission in Budapest with her then Handler (she thought the word with venom dripping in her thoughts) that she'll never say the name of, even in her own thoughts. One day. She thought darkly.

"Damn, these guys are good." Carina said, awed about these agents they were reading about, half an hour later of silent reading, pulling Sarah from her thoughts.

"Yeah." Zondra replied, nodding her head. "I agree."

"What's Project Omaha?" Sarah asked, silently agreeing with her two Squadmates.

Graham looked at Agent Walker for a moment, seeing how she was the one that picked that up.

"After the events of 9/11, the CIA and NSA were told to play nice with each other," He began, getting the three agents attention, "Omaha was the Project's Codename for an advanced computer called The Intersect. Every scrap of data we had, went into this computer. It mined for patterns, chatter, and saw things that we didn't. The data was encrypted into thousands of images. These subliminal images were then downloaded into those three agents that you have just read about.

"For a while, about five years, this team has done great things for this Country. The capture of La Ciudad for one, capturing several rogue agents, stopping a major drug cartel operation, made a chinese spy defect to the U.S., a Russian Operation, and recently, they are working on taking down Volkoff Industries and their subsidiaries."

"The major Russian Arms Dealer?" Carina Miller, DEA Agent of the CATs questioned, sounding impressed.

"The one and the same. What do you know of him?" Graham asked

"Only that this man's Industry is one of the top most weapons suppliers and manufacturers of the world. Rumors say that they're making some sort of handheld EMP device that can shut down half a city the size of New York."

"Yes," Graham nodded at Miller's information. "Currently these Agents were working on taking down a faction of V.I. known as The Ring. They've only been at this for a few months when their latest mission went sideways."

"What happened?" Agent Walker asked after a few moments of silence.

"According to the agent that contacted me, from what I can gather from his report, one of them was captured. The other two made an in-field decision to rescue him. Only they were too late. The captured Agent was turned, then attempted to kill his former partners."

"Shit." Zondra whispered. "And I thought we were bad." The other two nodded their sentiments, secretly glad they found the true mole on their own team and didn't ruin a great working relationship between the three of them in the process... and secretly their own friendship.

"So, what are we here for, Director?" Sarah asked after a moment.

"You three are being sent to Tunja, Colombia, where the two agents in question are currently held up. Your primary mission is to retrieve those two agents, and bring them back home. Secondary objective, if possible, is to find and capture the third one, alive if possible."

Carina leaned forward in her seat asking, "What do you mean if possible?"

Graham sighed a little, wondering if he should tell them the full Intersect story. He weighed his options for a minute, then nodded, coming to a decision.

"Not only does the Intersect have all the CIA and NSA data we've collected over the years, but over the past few years, there have been... upgrades to their Intersects." he finished warily.

"What do you mean by upgrades?" Zondra asked, slightly curious about this.

"Hmm... how to say this..." He paused for a few seconds, really thinking on how to explain, then, "Before their Ring assignments, we hadn't been lax on the original designs of the Intersect Computer for Human Interaction. We have been adding to the computer constantly, even adding Skill Sets as well."

"Skill Sets?" Sarah asked

"One of our contractors has been able to add Skill Sets to the Intersect computer. So basically, anyone can have combat knowledge, even if they didn't before. Anyone can be a doctor, even if they've never studied the subject, anyone can fly a plane if they haven't before, et cetera et cetera."

"Okay, that just sounds like something from a sci-fi novel or something." Carina said, not really sounding impressed. More bored than anything.

"I can assure you Agent Miller, it is very real." Graham said seriously. Then, "Your flight leaves tomorrow morning at 05:30. Dismissed."

With that, Graham looked away from the CATs to his monitor, and went back to work as the three nodded, stood, and left the Director's office to prepare for this rescue mission.

Tunja, Columbia, CIA Safe House

July 15th, 2007

He was freaking the hell out.

He couldn't before when he was rescuing his best friend and breaking out of a compound full of at least thirty Ring agents, maybe some Russians? and his former Partner.

His former Partner that had tried to kill him when he and his best friend tried to rescue the damn ungrateful bastard.

He was extremely lucky to have escaped that compound alive he knew. If he didn't have the Skills Set Upgrades, he knew for sure that he would've been screwed.

Currently he was pacing back and forth in the small living of the safe house trying to figure out what the hell went wrong during this mission. Everything seemed to be going fine up until a few days ago when his former Partner for some strange reason went off the reservation and went AWOL. He still couldn't figure out why though. He thought all three of them were tight, best friends even. Hell, they shared stories about each other even though they really shouldn't have because of their Spy life. Mainly for this reason.

"Oh crap, Ellie!" He said out loud as he paused in his pacing. He quickly grabbed his Satphone that he had modified to be smaller and more powerful as well (Hello, Nerd Genius!) and with a few bells and whistles. Like, activating a Cell Jammer and Scrambler app that he created himself that'll bounce his signal to be everywhere on the planet, making it extremely hard to pinpoint his signal, and also making his call as secure as a SCIF (Sensitive Compartmented Information Facility) Room. Quickly he made a call from memory, not really caring what time it was back home in Burbank.

Rii- "Hello?" Her voice answered before the first ring could finish.

Chuck paused for a few seconds, knowing he really shouldn't say anything, but was also glad that she was alright, for now.

"Chuck? Is that you, baby brother?" He heard her ask timidly, like she always does when he calls her on Holidays and their version of Mother's Day. Usually, he stays quiet for just under a minute (Tracing time usually picks up after a minute and two more minutes to get a trace on his signal without his security systems that is), but now?

"Hey sis." He said tiredly, sitting down on an uncomfortable seat. Seriously, couldn't the CIA afford better furniture for their Safe Houses at least? Then he pulled his phone away from his ear as he heard her squeal in happiness from the sound of his voice for the first time in years, wincing from said high octave sound as well.

"Oh Chuck, I am so glad to finally hear from you!" She said excitedly.

"That makes two of us El." Chuck said, putting the Satphone back to his ear. "I'm just glad you're alright."

"Why wouldn't I be alright?" She asked, sensing his tiredness. "Chuck, why do you sound like you've been up for thirty-six hours straight?"

"More like, uh," he checked the date and time on the screen of his Satphone, 'July 15th, 2007, 7:13pm', "Holy crap, I haven't slept in over seventy hours!" He exclaimed.

"What happened Little Brother?" She asked/demanded, and he swore he can hear the capital letters in Little Brother. "Did you stay up all that time playing video games or something?"

He wanted to laugh at that, if she only knew what I just did in the past few days. He thought.

Pause.

Hi, my name is Chuck Irving Bartowski. Also known as Charles Carmichael, Secret Agent for the CIA. Here's a few things you should probably know about me.

1. I graduated Stanford with flying colors, top of my class in Computer Engineering. Even got my Masters as well.

2. During my Senior Year (During Spring Break), both me and my College Roommate/Best Friend Bryce Larkin got recruited in the CIA. (Bryce admitted to me at the time that he thought about placing the answer sheet of a test I took under my bed and frame me for cheating, but we talked it out and decided to just join the CIA together).

3. My then girlfriend (Jill Roberts [known from then on as She-Who-Shall-Not-Be-Named]) for some reason dumped me via text. I also deleted her phone number from my records.

4. Bryce and I became partners in the CIA practically immediately and were sent to a DNI Research building where we met our third and final partner, a somewhat seasoned (He had at least five years on us green recruits) Special Agent Daniel Shaw.

5. It was here that we became The Intersect Team. Or just Team Intersect. T.I.T. just sounds weird. Ooh, or Intersect Team (IT Support anyone?... Anyone? I'll see myself out...)

6. The three of us then went on undercover mission after mission, pretty much each one of them a success thanks to the three of us all having Intersects in our heads. We bonded over the years, becoming as close as Brothers. At least, I thought we did. Until Shaw was captured and turned.

Back to the show!

Unpause

"No, nothing like that sis." Chuck replied after a few seconds had passed. "How can I explain this..." he groaned as he sighed, leaning forward in his chair tiredly.

"Usually the beginning helps." Ellie replied quietly.

"Not in this case big Sis." he said, rubbing his eyes with his other hand, trying to stay awake now that he was sitting.

"Why not?" She asked, "Stories usually start that way little bro."

"True, true, they do." he acknowledged, "But in my case, the story is sorta, kinda..." Well, he didn't want to say Classified to his sister, the one that basically raised him since he was nine when their mother left and then not long after, their father (by at least a few years), before he joined the CIA. You know what? Screw secrecy, she's my sister. He thought vehemently. With that, he took a deep calming breath like Shaw taught him to do, then, "Don't freak out sis." He said, taking another breath, then, "I'm a C.I.A. Agent, Ellie."

Nothing.

Still nothing.

"Ellie?" He asked, unsure if she was still on the line. He checked his screen to make sure the call was still going. He could see the seconds ticking up so yes, they were still connected. He put the phone back to his ear again. "Sis?"

"Come again Chuck?" She finally said sharply, "Because I thought you said you were a C.I.A. Agent?"

"Yeah. I am." He replied. Maybe this wasn't such a good idea... oh well, cat's out of the bag now. "Have been since Senior Year at Stanford."

Another long silence.

"C'mon El, the silence is killing me here." He whined.

"Well, at least you're still the same Chuck." She finally said with a sigh.

"What's that supposed to mean?" He asked warily

"It means, you're still my baby brother, spy or no. You're the only family I have left Chuck." Ellie said quietly. "And I promised dad that I'll protect you, no matter what. Did I ever tell you that?"

Chuck sat up in his seat at this, eyes wide in surprise when she mentioned their dad. "I don't think you ever did, El."

"It was a day or so after mom left and you accidentally broke her favorite necklace."

"Oh," He said, eyes widening. "Yeah, I remember that. Took us a few hours to fix it together with your art supplies."

"And we reverently placed it over Mom's photo." He could hear the sad smile in her voice at this. "So for the love of God Chuck, when are you coming home?!" She said, almost crying at the last part.

"I don't know if I can Ellie." He said, wishing he didn't have to say that at all. He truly missed his sister. Not being with her these past eight years was slowly eating him alive. The last time he saw and talked to her was after his Stanford Graduation Ceremony. "I'll try to make it to our Mother's Day. No promises though."

Something must have clicked for his sister because she suddenly blurted out, "That was you calling all those years on holidays right Chuck?"

Chuck just smiled, gave a tired laugh and replied, "Nothing ever gets passed you Sis. Yeah, it was me."

"Why didn't you say anything during those times?" She asked, and he swore he could hear the tears on her end.

"On missions. Couldn't really stay on long. But it was nice hearing your voice on those days, especially on our Mother's Day." Was all he could say. Because he really couldn't tell her about those undercover missions.

"Oh Chuck..." Okay, he can really hear her crying now.

"Hey, hey," He said consolingly, "I'm okay, okay Sis?"

"I know, I can hear it in your voice," he heard her say through tears, "I just really, really miss you little brother."

"Not as much as I miss you Sis." He said back, as he felt the tears coming to his own eyes. "Great, now you're gonna make me cry." He laughed and he could hear her laugh a little through the crying. This was when he heard a coded knock on the front door to the Safe House and he was instantly on alert again. "Gotta go Sis."

"Wait!"

"Someone's at the door," he whispered quickly, "And I'm not really expecting anyone. I'll try to talk to you later if I can Sis, I really gotta go. Love ya."

"Love you too baby brother." He heard the line go dead from her end and he looked at the timestamp on the phone for how long the talk was. He was surprised to see that it was about fifteen minutes or so. That had to be the longest he had ever talked to his sister in recent memory. Another coded knock on the door brought his attention again. Right, gotta see who this is. He thought, really hoping it wasn't his Former Partner/Mentor Daniel Shaw.