Introduction: Some of my regular followers who may be reading this are probably wondering why I'm working on this story instead of the next chapter of my current ZEXAL story, The Millennium Tournament. It's kind of a long story, but basically I was having some writer's block with the next duel for the aforementioned story when some stressful events regarding my current online class and other stuff in my personal life all seemed to happen all at once. Any drive I had to keep working on The Millennium Tournament was pretty much killed during those events. Another result was that I ended up more or less reflecting on the state of a lot of my current writing projects and whether or not I'll ever actually be able to finish some of them. Basically I kind of ended up in sort of a dark place.

Then a couple of weeks ago, something happened that rekindled my energy for my old GX Journeys project. So for the immediate future, I've decided to go ahead and get back to work on this series for the immediate future. At the same time, I'm also going to try and figure out a new and better way to balance my writing with all the other stuff going on in my life right now. Which means that updates to this story may be a little bit slow, but hopefully not by much. As for The Millennium Tournament, I'll get back to that story when I'm ready. Anyway, sorry for the long intro. On with the show!

Disclaimer: I do not own Yu-Gi-Oh! GX.

Prologue

It was fairly early in the morning as Dr. Alec Flynn stood in the control room of his laboratory. On the other side of the window he was looking through was a large chamber with metal-grey walls lined with pieces of electronic equipment. In the center of the chamber was a round grey pillar that had six blue metal pods with glass lids surrounding it. Inside the pod facing the window was the form of a young woman with long dark-blue hair wearing a white and blue Duel Academy uniform. This young woman was Blair Flannigan, a top ranked student from the Kaiba Corp Duel Academy who had volunteered to help with Alec's project.

Inside the pod, Blair appeared to be unconscious. But her mind was actually fully active inside a simulated virtual world made of ones and zeros. Blair had been inside that virtual world for the last five hours.

Alec turned to one of his assistants in the control room, a woman with tan skin and long dark hair sitting at a computer. "How's she doing, Rita?"

"Her vitals are still stable." Rita answered. "Everything is functioning normally."

Alec nodded and turned to another of his assistants in the right back corner of the control room, a fairly young man with dark skin wearing glasses. "Randy, can you tell how far along she is?"

"She's just cleared the second to last stage of the simulation." Randy answered as he looked at his screen. "I'm surprised she's gotten this far already."

"Chancellor Shepard did say he had sent us one of his best students to test out this simulator." Alec pointed out. "Still, I'm surprised she got this far so quickly considering how young she is."

"This girl's talent aside, this seems to prove that the simulator works." Rita pointed out. "It appears Mr. Kaiba's fears about this project were misplaced."

"Indeed. Now that the design flaws of Mr. Kaiba's original virtual simulation pods have been corrected, Duel Academies may now have a brand new training tool to us." Alec replied. "All we have to do now is wait for the current simulation to end."

Blair was walking through a desolate mountain landscape under a sky covered completely by thick dark clouds. She couldn't tell just how long she had been walking, though it had to have been at least an hour. During the whole trek, Blair had encountered several monsters that she either had to hide from or do battle with. She had hidden herself more often than going into battle on that level. All the monsters there were fairly powerful Fiends, and the battles with them had already taken her life points down to 2300. Considering that she was going to be facing the final boss of the simulation fairly soon, Blair knew that she needed to conserve as much of her life points as possible.

At long last, Blair reached the site of a large dark imposing castle. The young dueling prodigy pushed the large castle doors open and went inside, hoping very much that there weren't any nasty surprises waiting for her. Blair quickly found herself standing before a large staircase that she assumed lead up to the throne room. She went up there, thinking that the final boss would be waiting there. As Blair ascended the staircase, she wondered just who her next simulated opponent was going to be. She had already gone up against some of the strongest duelists from the original Duelist Kingdom and Battle City tournaments, which meant her final opponent was probably going to be a simulation of an extra powerful duelist.

As soon as Blair reached the top of the stairs, she pushed open the doors to the throne room. Inside, she saw a figure sitting on the throne on the far opposite side of the room. Blair walked inside, causing the large doors behind her to slam shut. The dueling prodigy flinched at the loud slamming noise of the doors, but quickly composed herself. She needed to focus if she was going to win against her next opponent.

"Whoever you are, I've come to take you down!" Blair declared. "So let's get this started!"

"Well, well. I certainly wasn't expecting you to be the one to come face me, Blair." The figure sitting atop the throne spoke in a very familiar voice. "This makes things even better for me."

Before Blair could ask her virtual opponent what he was talking about, he rose from his throne and stepped into the dim light streaming in through one of the windows lining the throne room walls. Blair became utterly shocked upon seeing who the virtual young man was.

"No… no way!" Blair exclaimed. "Dr. Alec said that…"

"You just challenged me to a duel, right?" the young man asked as he activated his duel disk. "I think we should get going."

Alec returned to the control room with a cup of coffee in his hand when he looked through the window and saw electrical sparks coming from Blair's pod. Red warning lights and alarm sounds began to go off inside the control room less than a second later.

"What's going on?" Alec asked his two assistants.

"Unknown!" Rita answered. "There's some kind of power surge and I can't find what's causing it!"

"I've just lost the data feed from the simulation!" Randy reported. "We're now totally blind as to what's going on in there!"

"Dammit!" Alec cursed. "It looks like we have no choice. Abort the simulation now!"

Randy tried pressing a large red button next to his keyboard three times, but nothing happened. "We can't! It seems we've lost all control of the system!"

"What about Ms. Flannigan's vitals?" Alec asked.

"Her heart rate's up, but she doesn't seem to be in any real danger at the moment." Rita answered. "Still, with the simulation now out of control, there's no telling what could happen."

"What do we do now sir?" Randy asked.

"You and Rita start figuring out a way to regain control." Alec ordered. "In the meantime, it looks like I'm going to need to make a few calls."

"You're going to inform HQ?" Rita asked.

"I don't really have a choice, now do I?" Alec replied. "The fact is we need help. If we can't get Ms. Flannigan out from the outside, then we may need to send people in to go get her."

Author's Note: I was actually a little hesitant to bring this story out, what with the "trapped in a video game" genre being a little bit overdone in anime and manga at the moment. Plus I've already done this type of story already with my currently ongoing Yu-Gi-Oh!/Sword Art Online crossover series, so I'm a little bit afraid of repeating myself here. Regardless, I'm going ahead with this thing since it's the story I feel like writing right now. I'll try to be as original as possible.

By the way, Alec's last name Flynn is a not-so-subtle reference to the Tron movies. Anyway, please review and let me know what you think.