First I want to apologize for the extremely long time it took me to get this chapter up. While I've had parts of this chapter planned out since the beginning of Fish and some even from early on in Do Over, when it came to actually writing out this final chapter of Fish my muse deserted me. It then began to attack me with plot bunnies for fic for Primeval which I have thus far successfully fought off. Regardless, I hope that now that I'm firmly back into season 2 territory and can look to the episodes themselves for inspiration and my muse will be more cooperative.

This will be the last chapter of Fish out of Temporal Waters. The sequel, my "Season 2" will (most likely) be entitled Chuck versus The Omega 302,850,000 after the Omega 13 device from Galaxy Quest. The device allowed one person to jump 13 seconds back in time. According to my calculations, Chuck was forced back approximately 302, 850,000 seconds at the beginning of Do Over.

As always constructive criticism is very much appreciated, whether it be about the chapter or about the next story's name. Thank you to everyone who has reviewed, I know I haven't gotten back to you like a should, but reading comments really are wonderful. Thank you to everyone who had favorite or alerted as well.

Chuck versus The Missing Pieces

September 26, 2008

When the other Sarah had suggested playing board games to wind down after missions Chuck had originally assumed she had just selected the activity she thought he would like that she could tolerate the most. It didn't take long, however, to realize that the other Sarah actually liked board games. She had her limits, of course, but then again so did he. While he had tried to keep it together for her during that two weeks they had been sidelined in the other timeline, inside he had been bouncing off the walls just as much as her. There was a reason he had been trying to encourage her to play video games with him instead.

The number of interests Sarah held outside of the spy world seemed few and far between, so Chuck was both amused and a bit relieved to find that was one aspect of the other Sarah's personality that was shared with Sarah here. Or at least he was when she and his sister weren't conspiring to crush his tiny plastic forces under their combined Walkertowski Empire.

Ellie had suggested a game night. It was unusual that all four of them had a night free and Ellie had wanted to take advantage of it. He was fairly sure either he or Awesome had suggested Risk, and now both of them regretted it. Despite how Awesome he was, Devon had already been assimilated into Ellie and Sarah's lands, leaving his own tiny parcel of cardboard as the final line of resistance before his sister and girlfriend finished conquering the paper globe, and began the civil war that would inevitably follow. As he looked out over their plastic armies, Chuck suddenly thought of Mal staring out over the opposing forces at Serenity Valley. Just as he was about to pick of the dice to begin his final stand, his own little plastic men were saved by the sound of his telephone.

Glancing down, he saw a text from Beckman. He looked up and gave his sister a slightly apologetic look.

"It's from work. The Nerd Herder on call tonight is in over his head and asked me to help with the call." He told her. Ellie looked a little sour at having her victory stolen from her, but seemed to understand. Awesome looked relieved.

Sarah excused herself, saying she wanted to tag along. Ellie gave her a questioning gaze, only for Sarah to lean in and whisper something that made his sister turn slightly red before joining him to head out to the car. Chuck decided it was better not to ask.

There was a slightly awkward silence as they rode towards the Orange Orange. Not because of anything between them, but because hearing from Beckman just served to remind them both of what they had both so far failed to do. They needed to tell Beckman what they knew about Leeryder. It was one thing when they thought a private company might be able to access other dimensions. But it was completely different when they now knew that an international criminal organization with whose agents had infiltrated virtually every government agency had schematics to weapons for an indeterminable number of universes and possibly for a machine to access more.

After a surprisingly short discussion both he and Sarah had decided that Beckman would be the one to tell. Despite her connection with Graham, even Sarah could concede that, based on what had happened in this and the other timeline, Beckman was more likely to be sympathetic.

The question was what to tell her. For the last couple of weeks while he had healed and Sarah oversaw the last of Castle's construction they had been stuck in limbo, unsure what to do. Anyway they looked at it, it seemed like they would be screwed. He didn't feel comfortable using any of the various back channels he had used to make "anonymous tips" in the past. His experiences had been far too hit or miss for something this sensitive. If they told Beckman that their knowledge about the incursions was from his parents they not only would be admitting to unauthorized and unreported contact with rogue agents, but would bring his parents under even higher scrutiny. If they told anything resembling the truth, he would most likely end up in a bunker somewhere being poked and prodded, while Sarah may well end up in a cell. That was if Beckman didn't simply put them in the CIA psychiatric facility alongside Merlin.

After they reached Castle, Beckman and Graham both seemed to be simmering in anger when they were pulled up onto the Castle's screen. Chuck was slightly relieved that the anger seemed to be directed towards each other. Beckman was the one that appeared to have the upper hand at the moment and began the briefing.

"As you were already aware, a few months ago Nathan Wexler acted as tech op on a black ops mission. What you were not briefed on, was that that mission was to retrieve information from inside Leeryder Industries." She told them. Graham, then continued.

"The founders of Leeryder Industries were both middling physics students until a few years ago. They specialized in a variation of string theory. At some point they decided to create an experiment to test one of the theories. It, according to the university, very literally blew up in their faces. They were expelled. Afterwards they moved across the Atlantic and started Leeryder. It wasn't until we saw some of the technology that began trickling out of the company that we thought there was any reason for concern. Several reports seemed to indicate they might be attempting to create something similar to an Intersect. The team Wexler was directing was sent to retrieve some of the equipment and a copy of the code from the second bank of computers you found on your last mission." At that point, Beckman's faced turned even more sour and she stepped in.

"I had been briefed that the technicians had determined that the servers were a failed attempted at downloading information directly into the brain, and that the items we had, had been destroyed. I have recently learned that was not the case. A CIA lab had been given the items and was attempting to reverse engineer the device." She practically spat.

"And what does the device do?" Chuck feigned curiosity.

"We now that the late founder's of Leeryder's experiments were more successful than their professor believed. We think they found a way to, more or less, sample information from different points in our timeline. And possibly from different timelines altogether.

Chuck didn't have to feign the shocked looked that over took his face.

September 27, 2008 (Early)

Casey had asked to be excused from the mission. The fact that he would ask to not to go on a mission after the team being inactive for so long, let alone one that was so potentially important had raised more than a few eyebrows, including her own. Then Sarah remembered that it was Alex's first week-end completely away from home. She really hoped that Casey at least had the presence of mind not to get caught spying on her. And that the frat boys this weekend were far less grabby then the ones during her own college days, if only for their own sakes.

The lab was unsurprisingly generic. It looked like pretty much every other secret government lab she had been to, which pretty much amounted, she suspected, to looking like any underfunded lab anywhere. Security was an eclectic mix of depressingly lax and obsessively complicated. The lab in which the actual device had been stored had a hand scanner on the door but there was only a few cameras in the building, most of which were focused on the one security station leading out of the complex. The hand scanner did, at least, narrow down the suspects considerably. While Sarah knew from experience that they could be faked, that still required someone to gain a copy of the entire palm print of someone who had access, and that most likely meant this had to either be an inside job or had been done with help from someone on the inside.

The thief's timing would, ordinarily, have been a very good one. Most people left quickly on Friday afternoons and the theft shouldn't have been discovered until Monday, giving whoever had stolen the items a two day head start on the investigation. Luckily for the good guys a particularly workaholic scientist had come back into the lab to verify a few of his readings and discovered that the interior of the device was gutted.

The last person who had accessed the lab prior to the one who discovered the theft seemed like the most likely candidate. At least to Sarah.

"He has a spotless record." Chuck insisted again as he gestured towards the screen. He leaned in slightly then. "And I didn't flash on him." The two of them had pulled up the records of the various scientists with access to the room and gone over their records. Chuck, for some reason, was resistant to choosing the easy answer.

"Not everyone is in the Intersect." She pointed out. "And he fits the profile. Overworked. Underpaid. Unappreciated. Money problems."

"I just think we're missing something." Chuck said, with a reluctant sigh. He gave her a thin smile. "But okay."

The first indication that Chuck was right, other than, well, him being Chuck, was when they knocked on the door and rather than having to burst in, the scientist simply opened it. He stood there, dressed in his pajamas, looking rather drowsy and not at all like someone who was planning to run off to an exotic non-extradition location with millions of dollars worth of stolen government equipment.

Then his wife joined them and Sarah realized that the reason he had taken a second mortgage on his house was because they were expecting. He even seemed more angry at the idea that someone had stolen the gadget he had been working on for months than at the fact that they were riffling through his thing.

She wasn't, therefore, surprised when Chuck tugged at her elbow and pulled her slightly aside.

"You were right." Sarah stated preemptively. Chuck looked briefly bewildered.

"I haven't said anything yet." Chuck said. She gave him a slight glare.

"We missed something. This isn't our guy." She stated dully. "The problem is, I'm not sure who else it could be. No one else entered or exited the room until our informant." She questioned aloud. Looking towards Chuck she saw him pause for a moment.

Sometimes watching Chuck figure something out was a bit like watching him flash. Or at least like watching him flash if he did so without looking like he was eating something sour and staring at something very bright at the same time. When the final piece of whatever he was pondering clicked into place, she could practically see the light go on, almost like one of those old cartoons.

"The informant." He said, slightly excitedly, before hurrying over to their back-up to give them instructions.

He caught her up on his hunch on the ride toward the second scientist's house. Chuck theorized that the other man had tried to frame his co-worker, or perhaps simply misdirect them long enough for him to get away. Sarah had been skeptical. After all, if it wasn't for the informant they wouldn't have known anything had been stolen until Monday. But as Chuck pointed out, their potential thief might be brilliant, but according to his record he wasn't very smart when it came to social interaction. Plus he may simply have had a grudge against the other man. Sarah decided, given that they had no other clues, to see how Chuck's theory played out.

When they got the new suspect's house, everything was dark. No one answered their knocks. Sarah stood back and allowed Chuck to moved towards the door. She decided not to argue that she could have simply picked the lock. Chuck seemed to get a certain thrill from kicking doors open. Inside was almost eerily quiet. They kept together as they swept the first floor, remembering what had happened when they had split up in France.

They found their thief lying naked in the master bed, with his throat slit. Chuck stepped out of the room quietly to call the others. Standing there she moved closer, taking a preliminary look at the body. The scene had immediately called to mind the one they had found in Shaw's hotel room. However, one look at the wound destroyed any thoughts she might have had that the two men had been killed by the same person. Whereas the wound on Shaw had been rough and jagged, created by a weapon of opportunity, this was one smooth, clean cut. Whoever had killed the man in front of her had known what they were doing and used a weapon designed for the deed.

Both they, and the back-up team searched the house. But whoever had killed their thief had already taken the parts of the device and disappeared.

September 28, 2008

Langston Graham sank down into the couch in his living room and began picking at the sandwich his wife had left for him in the refrigerator. He had missed dinner, again. He had stayed late to deal with the aftermath of the of the California team's latest mission. Not for the first time did he wish he hadn't agreed to that operation. And that woman, Beckman. He suppose he shouldn't blame her, she had no idea what kind of powder keg they were sitting on. That, at least, the CIA had been able to successfully keep secret even from the NSA.

Beckman had known Mary Gunter, when they were both young female agents in what was still more or less a boys club. She knew about Frost and that her former colleague had eventually turned traitor, but she didn't know that she was also Mary Bartowski, or that Stephen Bartowski was the infamous Orion the NSA had been searching for over twenty years. She didn't know that her new star team was headed by a time bomb waiting to blow up in their faces.

Chuck Bartowski was the child of two traitors. He had been raised by people who had maneuvered and manipulated the government into giving them exactly what they needed before going rogue. Stephen Bartowski had been a brilliant scientist. So brilliant that Graham's own predecessors had overlooked his flaws so that he would continue working with them.

Graham couldn't understand it. The elder Bartowski had conspired with a foreign operative. His known friend. He had given that operative classified government research and information without any kind of authorization and than that operative had gone on to use that information to create one of the more successful and deadliest arms empire in the world. And the brass before him hadn't done anything. They had gone along with his idiotic pleas that it was an accident because they wanted his research. Even once Bartow ski's wife went rogue and took another decade's worth of top secret information with her to become the main enforcer for Bartowski's former friend they had kept him on. It was only when they had finally closed out Bartowski's pet project, the creation of a human Intersect, in favor of a computerized model with limited human downloads that they had finally seen his true colors. Bartowski hadn't just left the project. He had gone underground and erased any way to trace him. It was then that they had realized that NSA had been searching for Orion for years without knowing he was CIA. That Bartowski had been going behind their backs and causing havoc with his own rogue mission for years.

When Graham had seen the current Bartowski on the list of possible recruits Fleming had sent to him, his knee jerk reaction had been to chuck the kid, pardon the pun, off immediately. But the old adage to "keep your enemies closer" was true and he elected to keep Bartowski as close as possible. If this was trap, he was going to be right on top of it, ready to spring his own. To his surprise it seemed that the younger Bartowski didn't have any clue who or what he parents actually were. That hadn't meant he let down his guard down. Even if the elder Bartowskis hadn't bothered to tell their children anything about the world they lived in, that didn't mean they wouldn't try to draw their son into their plans now that he had access, or that he wouldn't follow their example all on his own. And now he had the very thing in his head that the senior Bartowski had used to help set his "friend" up with an illegal empire to begin with.

Even if you were one of the exceedingly charitable people who believed that the fowl up during Bartowski's initial act of treason had been unintentional, that only meant that Bartowski jr. now had that same time bomb in his head. And Beckman was trusting him with the highly confidential information and a huge degrees of autonomy with only a has been Major that had long ago gone soft to reign him in.

Graham could admit he hadn't made the best choice of operative for the team either. He had thought Sarah's previous partnership with Bartowski would have hardened her against his peculiar but surprisingly effective form of charm. Instead she ended up sleeping with him. He should have known. Sarah had never met his expectation of her. Instead of her morally questionable background making her better able to deal with the grey area agents were often forced to work in, it only seemed to make her more sympathetic to those who hadn't been given the second chance she had.

Graham was beginning to contemplate setting up an accident for Bartowski. It was an extreme measure, and one he didn't take lightly, despite what his colleague might think of him. Especially given the possible help Bartowski might be in the fight against the Ring. But it would be worth it if I it stopped them from having to deal with another Alexi Volkoff, or worse, Mary and Stephen Bartowski.

Graham didn't, however, have a chance for his thought to precipitate into a more cohesive plan. Just as he contemplated his operative's deaths, the universe chose to demonstrate its sense of humor and a sniper's bullet tore through his skull.

XXX

As soon as she was sure she had made the shot, the sniper began to disassemble her rifle and wipe away any evidence she may have left on it. Despite how little she thought of her former employers she knew even they would be able to find someone who could trace the bullet that had killed their now former director to this apartment and this gun, the trick was making sure that neither was then tied to her. Given the circumstances, she doubted that would be possible, but she still wasn't about to take any chances.

Once she had cleaned off the last possible trace of herself from the area, she took just a moment to let everything sink in. Technically this hadn't been a revenge mission. Graham's death had been key to the Ring's current plans. They wouldn't have allowed her to kill him otherwise. But she also knew that they had given her this operation as a reward for her recent activities. The man whose brains she'd just splattered all over his overpriced wallpaper wasn't the one who had ordered her death. But she had no doubt that if this Graham had had the same information as the one in her dimension, he would have made the same decision. That was enough for her to feel that she had gained some measure of justice with the recent shot.

She moved over towards the mirror and made sure her chosen disguise was on correctly, then brought her hand up to kiss the two entwined rings on her left ring finger. They weren't, strictly speaking, her wedding rings. These ones had been exchanged as part of the ceremony between the her of this reality and the sick twisted version of her husband that she had found herself with when she had woken up in this reality in Leeryder's lab. But they were the closest things she had to a memento of her own beloved and she hope that was enough for them to give her a bit of luck. Taking a breath she grabbed the bag containing the only part of her equipment she was bringing with and headed out.

September 29, 2008

Chuck was woken up to the sound of his radio alarm. He quickly reached over, trying to stop the blaring Huey Lewis song from waking up Sarah. Looking over, he saw her stir next to him, but she seemed to be still asleep. Quietly he slipped out of bed and headed towards the bathroom. After turning on the shower he reached over to lock the door, but paused a moment. Ellie and Devon should still be sleeping off their last long shift at the hospital and if he was wrong and Sarah was waking up, he really wouldn't mind running a bit late to work if it meant she joined him.

Chuck shed the boxers and t-shirt he had had worn last night and headed into the shower. A few minutes later he was rewarded by seeing his beautiful, slightly drowsy girlfriend stumble into the bathroom after him. He smiled as he watched her perform a bit of an impromptu striptease on the other side of the already fogging glass before stepping into the shower beside him.

He had already mostly washed already and decided to take it upon himself to help Sarah, scrub. They were so involved in scrubbing that they didn't hear the soft click of the door opening again. Sarah did, however, hear the squeaking of someone clearing off the misted mirror, and quickly dove to stand behind him. In the now clear glass he saw Ellie's eyes widen slightly as she saw their reflection, before she covered her face with her hands and screamed. He could feel Sarah's whole body seem to grimace behind him as his sister ran out babbling about being blinded.

"We really need to start looking for our own place." He finally said. He felt Sarah's head nod against his shoulder from where she still hid behind him.

After quickly, actually, scrubbing down they both threw on clothes and headed awkwardly towards the dining room. Devon, apparently, was also already awake. He looked perfectly at ease, and even gave Chuck a bit of knowing smile and a slap on the back while Ellie sat stiffly at the table holding her coffee cup almost protectively as she attempted to look everywhere but at him and Sarah.

After the two of them sat at the table there was an awkward silence for a few moments, until Ellie finally spoke, keeping her eyes firmly away from her brother.

"Your phones both rang when you were." She floundered a second. "When you were getting ready." She said, before taking another huge gulp of coffee. Chuck glanced towards Sarah, and they both excused themselves and headed towards their room. Beckman had texted both of them to go to the Castle. After a rather uncomfortable round of goodbyes, they headed out.

The fact that Beckman was the only one on the screen when the briefing started wasn't unusual. The look on her face was. She almost looked nervous.

"Director Graham was shot and killed at his home earlier today." She said, without any real preamble. Chuck's eyes automatically darted towards Sarah. Despite his own feelings towards Graham, the director had still been very important to Sarah. He had been her mentor and had saved her, both from her father's enemies and from falling in her father's footsteps. He saw her wince slightly at the news, before standing up again, a bit too straight and a bit too impassively.

"When are we leaving for Washington?" She asked Beckman in an even tone.

"You are not. The FBI are handling the investigation." Beckman stated.

"You can't be serious." Sarah said in disbelief.

"In case you've forgotten Agent Walker, the CIA do not have jurisdiction domestically." Beckman said warningly.

"That's never stopped you from assigning us an investigation before."

"Not for something as high profile as this." Beckman answered back, before adding more gently. "I think you'll agree we don't want whoever killed Graham to avoid their due punishment because of a technicality?" Chuck glanced over. Sarah screwed up her lips into a sour expression, but nodded. Beckman sighed, suddenly looking weary, before her face softened slightly.

"I can tell you this. The FBI found one sample of DNA in the apartment they believe the shot came from that didn't match the late owner. It didn't register on their databases, but we were able to give the sample to our technicians and they found two partial matches in our own databases."

"What exactly does that mean?" He asked.

"There are a number of people, Agents or those suspects who we don't want the local authorities to attempt to contain whose DNA are only in our own database. It could mean that the culprit is the child of two of these individuals. However, in this case, given who the matches are and how the genes are arranged that seems unlikely." Beckman told them.

"Why?" Chuck asked, warily.

"Because DNA was a partial match to both Laura Cleary and Evelyn Shaw."