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Enjoy!

FYI: 'thought'

"Dialogue" Just in case you were confused about the punctuation. :)

Disclaimer: I don't own anything, or else Chuck would probably still be on the air.

Chuck vs the Intersect Charges

Somewhere in the middle of nowhere

Quinn tied Chuck to a chair in the middle of a random warehouse and waited for him to wake up. Chuck regained consciousness after a while and he looked around taking in his surroundings when he saw Quinn. He suddenly realized that he was tied to a chair and Quinn was picking something up from a table.

"What the hell are you trying to do Quinn? You must know that you won't succeed in anything that you try to do to me." Chuck said as he reached for a star that he had hidden in his back pocket.

"Oh but the thing is I know a lot about the Intersect, probably not as much as you, seeing as your father was the creator, but enough to know how to control it. These pieces of paper are Intersect Charges and well... they make you flash." Quinn said as he showed Chuck the pieces of paper.

As soon as Chuck saw the charges, he started to flash uncontrollably. Each time he flashed a little bit of his memories was suppressed.

First the wedding, General Beckman, then Prague, all of his missions, the Intersect, Sarah, Casey, the Buy More, Jeff, Lester, Big Mike, Jill, Morgan and Ellie and Awesome, and finally his parents. The Intersect only suppressed the memories that gave Chuck emotions while he had all of his motor skills, but the Intersect didn't suppress Bryce Larkin as he was a source of hate and his computer skills, to allow him to be able to survive in the real world.

Chuck dropped his star during the first flash and blacked out after Quinn stopped using the charges. Right before Chuck slipped into unconsciousness, Quinn put suppression glasses in him to suppress the Intersect just in case Chuck ever got his memories back. A few hours later, Chuck woke up in a hotel room somewhere in Burbank. He looked around the room, taking in his surroundings while stretching and getting over that just woke up laziness feeling. He saw that he was in a hotel room and thought to himself puzzled. 'Why the hell am I in a hotel room. Wait a second, I don't even remember my own name. That's odd.'

Suddenly the door opened and Quinn walked in, surprising Chuck which inadvertently set off the spy instincts that Chuck had retained from his training in Prague. As soon as Quinn walked in Chuck used a pen from the table and stabbed Quinn in the shoulder before using Quinn's coat to put Quinn in a choke hold.

"Who the hell are you and what do you want?" Chuck asked as he systematically cut off Quinn's air supply.

"I'm...h...her...here...to...off...offer...yo...you..a...jjooobbb." Quinn managed to cough out through Chuck's choke hold.

"Oh really?" Chuck asked as he let go of Quinn, "Sorry, you just startled me. Oh by the way, would you be able to tell me my name?"

"Ummm... Must be the amnesia. Okay so your name is Chuck and you are currently in training to be a member of a joint NSA, CIA team whose purpose is to execute the most high level missions. Anyway on your first solo mission, you were attacked and almost killed by a rogue spy by the name of Sarah Walker. She and her team got to you and pushed you off a three story building, you hit the ground and Walker and her team left you just lying there, probably thinking that you were already dead. You were sent to the hospital and you have a bad case of amnesia, sadly we've had no progress in bringing back your memories." Quinn explained.

"Okay so what are you doing here right now." Chuck asked intrigued by his past.

"Your mission is to take out Sarah Walker's team. Here is a picture of Walker and another picture of her team." Quinn said as he showed Chuck a picture of Sarah and Morgan, Casey, Alex and his family, "I'm here to train you to better prepare yourself for when you face off with Walker and her team."

Chuck picked up Sarah's picture and looked at it with a fine tooth comb. He thought something looked very familiar, but ruled it as he had researched her many times and just pushed it to the back of his mind.

"Okay... Wait hold up!" Chuck said as he looked at the picture again and saw a gorgeous blonde angel, "Why would I kill someone so beautiful and harmless?"

"Charles Irving Bartowski! She is a rogue agent and is about as harmless as a hungry tiger! Killing her and her team is doing your country a big favor and is a good deed." Quinn said, "Training starts in a few minutes. Follow me."

"Okay... Fine. You don't have to be so pushy." Chuck said.

In an abandoned Underground CIA Training Facility

After a few hours of training, Chuck was exhausted and still couldn't do some advanced katas, that he had been working on for hours, his throwing skills were okay but could be improved, and his shooting skills were mediocre if not horrid at best.

"Why the hell am I learning to shoot a gun! I can't use a gun. It's wrong to take someone's life." Chuck said as he looked at the gun in his hand with disgust.

"Chuck, this is for your own good." Quinn said out loud before whispering to himself, "I don't think Walker had this much trouble with that annoy runt, Bryce Larkin, that messed up my life."

Quinn had whispered just loud enough for Chuck to hear the whole thing and a new feeling sprung up in Chuck.

"Did you just say Bryce Larkin?" Chuck asked as he gripped the gun in his hand with intense anger.

"Yes, yes." Quinn answered before going on seeing the flames of intense anger that were blazing in Chuck's eyes, "Bryce Larkin was the partner of Sarah Walker and he was the mastermind behind the whole plan to take you out. You were able to take him out the same night that you lost your memories, but Sarah and her team will want revenge. You want to be better that Bryce right?"

After Quinn finished his Larkin rant, he saw a great change in the way Chuck took his training. Chuck sped through his training, accomplishing a lot more progress than most high level agents. Chuck actually tried to learn what he was taught. His martial arts excelled and he learned everything that the trainer could teach him before they used the internet to teach him others, his throwing and silent killing skills went off the charts reaching new highs that left everyone with big eyes and dropped jaws, as for his shooting skills, he went from mediocre to pinpoint accurate in two days. He could hit the wing off a fly from a hundred yards away with a simple pistol without even using a scope. He had gone from a average agent with the Intersect to a deadly and cold-hearted assassin without the Intersect in a matter of days.

This little fact was the source of Quinn's happiness and worst nightmare. He loved that he had control of, most likely, the world's most deadly assassin, but he wasn't sure how long he was going to be able to keep that control. He was able to see that the only emotions that Chuck had now was hate and he was becoming distant. This Chuck was never going to be able to pass on as the old Chuck that was a lively and very caring individual. The family and friends would be able to spot the problems with him almost immediately and that would be counterproductive.

Chuck was finishing his training when Quinn walked over to him. Chuck quickly finished and went over to Quinn to see what he wanted.

"Quinn, What do you want?" Chuck asked seeming to be annoyed.

"Chuck, your training is finished and it is time for you to go back to your mission. Your job is to infiltrate and make friends with them, then when the time is right, take them all out. But you're going to need to reconnect with your lost emotions. Okay so your story is going to go like this..." Quinn said.

Echo Park, California

Apartment Complex where the Bartowski's reside

"I'm going out to find him! We don't know what the hell Quinn is doing to him and I don't want to think of what might have happened to him already." Sarah said as she rose from her seat in the living room of the apartment and she lived with Chuck in.

"Walker, if you're going then count me in. The kid has helped me out over the years and has served his country with honor. I believe that he is a very honorable man and I'm not going to let a traitorous son of a b**** like Quinn just rip him apart." Casey said in his gruff voice as he pulled out his pistol.

"Sarah, I'm coming along, too. I lost my family twenty years ago and I lost Stephen to a turned CIA operative. I'm not going to lose my son to another one if I can help it." Frost said as she also pulled out her pistol.

"Casey, MOM! Not Awesome. What did we say about pulling firearms out in front of baby Clara!" Devon AKA Captain Awesome yelled, "besides I think that you should plan this out more, not that your plan isn't awesome, but going blind isn't as good as knowing where the hell he is."

"Sorry," Casey apologized, though he really wasn't that sorry.

"I'm so sorry! Did Nana scare you?" Frost apologized as she cooed at her granddaughter.

"That isn't the point! We can research him on the go and besides every second that we wait, Chuck's chance of ever returning decreases!" Sarah yelled as she started to walk out of the room.

After Sarah said that, the door suddenly opened and in the doorway was the one person that they never would have believed would be there.

AN:

Well this is the end of the third chapter. The first two chapters were almost a carbon copy of the actual episode and this chapter had some elements but I can assure you that the rest will be pretty much all new and original.

I hope that you like it!

Please review!

Thank you for reading!

Dragonslayer9907 signing out.