Chapter One

Purgos was a city that had always been considered a boom town before Clu's takeover. Filled with the prospect of new jobs and opportunities that programs had never been given, they flocked their in numbers. The city had fallen into disrepair when Clu overthrew Flynn. Soon, it became nothing more than a garbage heap.

When the Son of Flynn had restored the Grid, he also rewrote the files regarding Purgos. Shadow eyed the city warily as she reached it, turning her light cycle back into a baton. She knew the layout of the city like the back of her hand. Equipped with grenades that would prove an effective way of destroying the city, she searched for the weak spots in question.

Programs eyed her suspiciously when she maintained a straight face throughout the procedure. She'd been careful enough to put on a disguise so they wouldn't recognize who she worked for. Dyson had warned her that Tron had followers, and from what it looked like, he was right.

She leaned forward, ready to attach a grenade when a program spotted her. Shadow stiffened from the initial stares that were thrown in her direction. Debating whether or not she should make a run for, she instead hid the grenade where the programs wouldn't see it. She knew they wouldn't hesitate to take her down if they saw the grenade in her hand. She had to strike in an area that wasn't so heavily populated with programs.

"What are you doing in the outskirts?" he asked, eyeing her up and down warily.

"I was sent here to survey the buildings and make sure they were up to code," she explained, keeping a straight face when she stood up and reached for her disk out of sheer instinct, "I'm an architect."

The program just rose an eyebrow, looking more than skeptical with her explanation. Letting out a sigh, Shadow pried her disk out of place and opened a few files, sifting through the memory banks she'd created. Dyson was the one who told her of her capabilities. According to him, she was programmed to redesign the Grid, and she could also modify whatever code she could by manipulating it. She wasn't entirely sure why she was gifted with so many abilities. Dyson had explained to her that the abilities she retained were a gift from Clu, who sought to use her as a method towards peace and perfection over the Grid.

"Looks like everything's in order, here," the program said uneasily after reading through the files. "Just make sure you're quick. A few of the programs around here are already uneasy as it is with all these disappearances happening, lately."

With a nod of agreement, Shadow resumed her role of observing and surveying the safety of these buildings. She waited until he was gone before placing the grenade at the weakest structure. A few more microcycles of this went by before she finally rezzed her light cycle and headed towards the outskirts of the city. She couldn't wait to see the look on Tron's face, or anyone else who followed him. They were in for a nasty surprise, as far as she was concerned.

…

The Grid was finally in a state of peace. The cities were now protected by programs who were trained personally by Tron. Sam Flynn managed to recreate the Grid in a way that was even better than the original. He wanted to give programs a chance at life that Clu had stripped from them when he took over. He was determined to live out the dream his father had envisioned years ago, without the problems caused by Clu. He'd even added a new feature that gave programs the chance to see what daylight was like, along with numerous other times of the day that occurred in the Real World. Overall, everything should have been perfect.

As was the way of things in life, the peace that followed didn't last long. Programs had gone missing while they were out on patrol. Tron didn't want Flynn or anyone else to find out until he figured out why this was happening in the first place. Part of it was his own stubbornness to prove that he could handle this on his own. Though, if Beck were being honest, he knew that this was something they needed help on. Something was clearly wrong, and, something told him that it would only get worse if they continued ignoring it.

Beck himself kept his distance from the programs who worked at Able's garage. They were not only working at the garage, but, they also were part of a small force to protect Argon City, home of the new headquarters. He couldn't bring himself to face them, even after they had learned to accept that Tron was still alive. Some small part of him was terrified that they would turn their backs on him. He still had nightmares every now and then, of things going horribly wrong.

It amazed him how much programs had changed since Flynn redesigned the Grid with Mira's help. Thanks to them, programs could finally see what a sunrise was like, and a sunset. It had shocked them at first when they realized what the sun was, but eventually they learned to accept that as well. The biggest change though was the fact that programs had begun to accept Users into their lives. Though some were still prejudice against Users because of Kevin Flynn's mistake in Clu, most of them had begun accepting the fact that Users were the reason they existed in the first place.

The only problem with Mira working alongside Sam and Quorra to redesign the Grid was that she didn't spend as much time here. Beck hadn't seen her for two mylacycles, and he was beginning to wonder if he would ever see her again. On top of working with the Son of Flynn and an ISO, Mira was constantly busy spending more time with Natasha and Clint, her biological parents. He supposed he couldn't blame her for wanting to spend more time with the Users who had finally accepted her as their daughter.

It was just difficult, knowing that they were two worlds apart. Literally. He always knew that Mira being a User would only complicate things. But, it had never been a problem until she started spending more time in the Real World.

"You're going to derezz if you don't get enough energy." Beck nearly leaped out of his suit at the sound of Paige's voice. The former commander smirked in amusement at his reaction and sat down beside him. "You know, it helps if you talk about your problems," she added.

"Is it that obvious?" Beck frowned when he realized that he'd probably looked like a wreck.

Honestly, he'd been working himself to the point of exhaustion every cycle. It kept him distracted from thoughts of the Real World and what Mira could be up to. At least, he hoped that it would keep him distracted from those thoughts. Of course, it hadn't helped much when he kept imagining every worst-case scenario that could happen to her.

"You're thinking about her again, aren't you?" Paige asked, and Beck let out a sigh before nodding. "She's been awfully busy lately, but I'm sure she'll find time to stop by and visit. You know, she actually isn't all that bad… considering she is a User."

That was enough for Beck to narrow his eyes in annoyance. Paige was one of the few programs who hadn't really gotten used to the fact that Mira was a User. He couldn't help but wonder how many other programs would act the same way; they never once gave her a chance. Programs shied away from her because she was a User, and, all the lies and rumors that Clu had spread about them hadn't helped matters.

"She's more than just a User," he snapped irritably.

After everything they had been through, he wouldn't let anyone talk about her as if she was nothing. Mira was so much more than just a User. She had proven time and time again that she was stronger than anyone realized.

"I know she is," Paige murmured thoughtfully. She looked down at the floor, her eyes narrowed as she tried to recall something from her past. "She was the one who saved me from Cyrus. I know that I should be grateful, but sometimes… I wonder if it was worth saving me," she sighed.

He stared at her in surprise when she said that. Paige was a complicated program. From day one he had always liked her, and wasn't afraid to admit that at one point, he had feelings for her. She had a fiery spirit in her that would always burn. But it was only because of what general Tesler had done to her friends in the hospital that she was that way. He wondered if she would be any different had fate worked differently that cycle.

Neither of them had discussed their relationship after she chose to leave for Bismuth, and Beck had left with Mira through the Portal. The same unspoken kinship he felt towards Paige was always there when the Grid was restored. She fought alongside him when Mira couldn't, and had proven to become an invaluable partner.

She was about to leave when a light cycle suddenly approached them. Paige stopped in time to see Tron pull on the breaks, and his mask receded. He didn't look happy. Then again, Beck had rarely seen Tron actually look happy. Tron looked at Beck, his expression serious as ever.

"We have a problem," he told them.

Paige exchanged an anxious look with Beck, who only seemed more worried than before. Just when it seemed like the Grid was finally at peace, things seemed to spiral out of control. Beck knew that the peace would only last for so long. With problems consisting of Gridbugs and viruses, there was always something they had to worry about.

"And, I'm guessing it isn't anything good," he muttered, brushing the back of his hair with his hand.

Tron only glared at him in response before leading the way to HQ. Headquarters was actually where Tron used to keep the safehouse, but it was upgraded to a much larger building to house so many programs. From here this was where Sam Flynn would meet with Tron and discuss whatever needed fixing or whatever was needed in general. It was also the only place where SHIELD could keep in touch with Tron if things got dicey on the Grid.

Tron led them into a room where a monitor overlooked the Outlands, just like the original safehouse. Paige rose an eyebrow upon seeing the SHIELD logo on the corner of the screen. She had met Natasha and Clint once or twice, and they hadn't seemed like bad Users. But there was especially something about Natasha that she couldn't trust. Paige hadn't spoken much about her lack of trust in the redhead, but Beck suspected it was because Natasha looked so much like Mira. Both were cold and distant towards those they didn't trust. They acted so similar in so many ways that it was almost uncanny.

The moment they arrived in the room was when Beck realized they weren't alone. His anxiety turned quickly to panic when he saw Natasha and Clint waiting for them in the room. Paige's eyes narrowed as she realized something serious must have happened if these two were here. Neither rarely showed up unless they had some serious news to share from the Real World, or talk to Mira when she wasn't with them.

"Alright, security monitor, where is she?"

None of them had a chance to answer Clint's question when an alarm suddenly sounded. Beck couldn't imagine what was worse than having two highly trained SHIELD agents in the room until seeing what the alarm was blaring for. Tron had already opened the security footage, eyes widening in horror when the images became clear enough for everyone to see.

Paige let out a gasp of utter shock when she saw the state that Purgos was in. Sam had reworked the Grid so that every city destroyed by Clu was redesigned. After seeing the mess the cities were in after Clu was merged with Flynn, Sam wanted to reassure everyone that they would all have a place to live. Most of the programs had been wary with the idea of having decent cities to live in, but once they found out what Sam was capable of, they jumped at the opportunity. But, that didn't do the programs in Purgos any good when half of it was destroyed.

Beck felt his stomach twist with disgust when he saw pixels coating the ground where programs once stood. It looked like a scene from a horror movie. He wasn't sure what would have led a program to destroy a city like this and take out so many other innocent programs. The only thought that crossed his mind was how cynical Clu had been before he was finally taken care of. And Cyrus was another insane program who was also locked in a prison in the Real World. So that didn't leave him with too many options of guessing who could be responsible for this mess.

"So, I take it the Grid isn't 'at peace'," Clint scoffed when the security footage stopped. "You wanna explain what the hell's going on?"

Tron only rolled his eyes before playing the video back and zooming in to get a better view of the destruction. Beck hadn't missed the fact that someone was standing at the top of a building, their arms crossed in satisfaction as they watched the chaos unfold. What had sent shivers of fear through him were the words coated in blue pixels across a fallen building.

"COURTESY OF YOUR OLD FRIEND."

…

Shadow couldn't help but grin at her triumphant work. Those blue pixels were really what had brought out the best in what she did. Using Free Code and whatever bits of data were left from the programs she'd derezzed, she spelled out a clear message for all to see. It was meant as a warning to anyone who thought of arguing against Dyson's methods, or fighting against Clu's vision of perfection. Once she was certain that there was only one survivor left to tell the tale, she returned to the base.

Dyson had bases scattered throughout the Outlands. As a secondary precaution, he had guards placed within every base. Tron's enforcers had come close to finding the bases, on more than one occasion. Shadow remembered hearing him mention that Tron was determined to bring him down, and continue spreading chaos and lies throughout the Grid. Fortunately, the main base wasn't all that difficult to reach. All of the bases eventually led to his main throne room where only the highest and most trustworthy and loyal soldiers worked. The nanocycle she had returned was when she saw Dyson already waiting for her.

"You did well," he reassured her when her mask receded. Dyson had warned her that programs might try to take advantage of her if she showed her face. So keeping a mask on was even more important, especially when these missions took place. "Purgos will soon understand why it had to be cleansed." Shadow simply nodded in agreement and tossed him her disk, so that he could see for himself what sort of damage was done. His smirk only grew wider as he saw the words that were left to warn any program of their keen work. "I like your particular choice of words, and the fact that you left one survivor."

He promptly returned the disk after sifting through her memories.

"Well, I figured the scare tactic would work wonders," Shadow replied with a shrug. "It's amazing how effective it can be, especially when said program is already a weak architect to begin with."

"Good work, soldier. Now, get some rest," Dyson told her. "I'll be sure to assign you to the next mission when the time arrives."

Shadow simply nodded at that, taking orders like any good soldier would. As she left, Dyson was left in awe of the amount of time and effort she had put into destroying a single city. He never would have imagined that this was the same User Clu had tortured xilacycles ago. Or the same User that had fought with such ferocity a mere few cycles ago. It was almost pathetic, in a sense, what repurposing could do to someone.

Truthfully, what Zena had said left him feeling a bit worried. Clu had experimented on the User. He gave her enhancements that few knew about. Dyson was able to make out a few of them, such as inhuman strength, agility and natural healing. That was only a small portion of what Dyson could make out.

"I don't like this," one of the soldiers whispered as Dyson approached, not noticing his arrival until it was too late. "Something about that soldier doesn't feel right."

Dyson stopped for a moment and smirked as the two soldiers stiffened with fear. But just for a quick nanocycle, Dyson decided to humor him. His state of calm was what had driven most of the soldiers into fearful obedience. Even they dared not make attempts at angering him. While he didn't show his anger, often, they knew when he reached that point.

"And what, may I ask, doesn't feel right?" he asked, feeling genuinely curious.

The soldiers blinked in confusion at the oddly pleasant tone he spoke in. This was not the Dyson they were used to, and they were suddenly wary of his imposing demeanor.

"The User, sir. Something about the way she's acting… keeping her in our ranks. It just doesn't feel right," he explained with a shrug. "It just feels… unnatural."

Dyson's look of amusement turned to a scowl of disgust. That User was his weapon. His tool to cleanse the Grid of imperfection. She may not be aware of his plans now, but, she would be soon enough. She was changed into his view of perfection. And nothing would ever change that. Not even Tron or the Renegade, who seemed so determined to keep her and the Grid safe.

Without wasting a nanocycle, Dyson reached for his disk and activated it. The soldier wasn't even given the chance to react when he suddenly sliced the disk across his stomach, leaving a deep gash. Nanocycles later, pixels scattered along the floor, leaving his partner gaping in utter horror.

"I want this mess cleaned up immediately!" Dyson snapped to the soldier who had watched in appalled horror. "Let this be a warning to anyone who dares question my motives," he added in a dangerously low tone.

The soldier was all too willing to comply with nothing left to say. Once he had left to clean the floors, Dyson nodded in satisfaction. This was exactly what Clu would have wanted. To strike fear in the eyes of his soldiers, and inspire the programs who seemed to oppose him. One way or another, programs would see things his way.

…

Mara bit the bottom of her lip as she studied the complicated code in front of her. A few cycles had passed since she was asked by Able to fix this light cycle. The code had become corrupted after the rider drove through the Outlands and was ambushed by Gridbugs. Apparently, the Gridbugs themselves had carried bits and pieces of codes that turned the light cycle into a mess. The good news was, Mara and Zed were working together to fix the code so that it wouldn't malfunction again.

"… can't believe Purgos was left in shambles." Mara flinched when she heard Zed and Link talking as they arrived late for work, as usual. "And now Tron's letting those Users stay. I don't know what's fishier."

"I'll admit, that red-head User terrifies me," Link muttered. "Did you see the way she was glaring at everyone?"

"What happened in Purgos?" she asked, standing up after realizing something had gone horribly wrong.

Mention of Users made everyone feel uneasy. Even if the Son of Flynn had recreated the Grid, there were still some programs who weren't overly fond of Users. It left a bad taste in everyone's tongues as they remembered the malicious lies that Clu once spread on Users. Though, Mara wasn't willing to admit that she would have been the first to turn the User that Clu had captured all those cycles ago. That User in particular, who had also been seen with Beck at one point or another, had unnerved everyone.

"Someone destroyed the entire city," Zed explained after he realized she'd heard almost everything. "And on top of it, those two Users that were with the Rogue decided to return."

Now, Mara understood what the problem was. Zed had a nasty run-in with the Users who were somehow related to the Rogue when they first arrived on the Grid. Ever since then, he had tried keeping his distance from them and the Rogue, for good reasons. Then again, there was always something about those Users that had always left everyone feeling uneasy. The redhead in particular always left Mara wondering if they could be trusted.

"Isn't Tron supposed to watch out for threats like that?" Mara asked, narrowing her eyes as she wondered how anyone could do such a terrible thing.

"Yeah, but this was something even he couldn't track down," Link told her, suddenly aware of the danger they were all in. If one city fell, it wouldn't be long before they all fell. "I just knew that the peace was too good to be true."

Mara didn't really blame Link for feeling so worried. She may not have been around long enough to know what it was like before Clu took over, but something very similar was happening right now. If another program who followed Clu's ideal for perfection was still alive, they would surely start by striking fear in the hearts of programs.

"He isn't going to take this sitting down," she decided out loud. Zed and Link looked at her in confusion. "Tron. He wouldn't let programs suffer because of one reckless action."

Both mechanics could agree with her on that one. Knowing full well that Tron had set his sights on the program responsible should have made them feel better. But Mara couldn't shake off the feeling that this was only the beginning of the chaos that would follow. Something far worse was going to happen.

AN: Well, there's the first official chapter. I know that it's choppy and has quite a lot of scene-skips, but, I wanted to add as much as possible into one chapter. Almost all of them will probably feel like that, unfortunately. I also apologize in advance for how slow my progress may be in updating. I'm actually taking my time with this story as much as I can; I want everything to fall into place, unlike the original, which had quite a lot of loopholes in it. So, with that being said, thanks in advance for your patience, and, to Flicka the Light Beast for reviewing!

Flicka the Light Beast - Thank you for reviewing! I have checked out the first chapter of your story, and do find it interesting. Though, I would recommend moving it to the movie section rather than the show. You'll actually get more viewers, that way. Sadly, most people don't even know there's an Uprising section on this site. Thanks again for reviewing, it's appreciated :)