This is a crossover with a samurai anime you might know, but I won't tell which one it is until you get to the end. If you know the anime, you might be able to figure it out from the title.
Deeper Duelist
A stranger shows up in Domino City who claims to know the "true future," and Pegasus is not a part of it.
It was of utmost importance that Yugi wage this Duel, even as Joey insisted that it was only Pegasus' life that was on the line. Even though Pegasus had once upended Yugi's life and tormented his grandfather, it just didn't seem right for the King of Games to sit idly by while a stranger ended the father of Duel Monsters. Yugi had his honor, after all.
Apparently this man had his own brand of honor to contend with, which seemed odd, considering the death threats. "You don't understand," he shouted as Tristan struggled to fit the Duel Disk around the many barrels of the man's revolver. "Pegasus has to die!"
The Duel Disk finally clicked into place with a heavy-handed shove. Though it looked ready to fly off at any second, Tristan had played his part, and he didn't want to stand next to the man for a second longer than he had to. He handed the man the deck that Yugi had constructed for him on the fly, and stepped back as the man continued to rant and rave.
"I've seen the future, and this is not as it should play out!"
"I don't care what kind of future you claim you've seen!" Yugi replied. "You're not hurting anyone while I'm around!"
"So be it." The man held out his Duel Disk in preparation for the coming battle. "If you won't listen to reason, I will beat you at this 'Duel' and win the right to correct the future."
"That's what you think." Yugi spread his feet and activated his own Duel Disk. A small part of him wished they could be Dueling in one of the back rooms at KaibaCorp. It would have been easy to call in the favor wth Kaiba, but Pegasus hadn't given them any details over the phone. If Pegasus had been a little more specific about the "urgent threat" he needed help with, Yugi and his friends might have stopped to think about what they were going to do before rushing over. They had thought he was being murdered, which he technically was, or at least he was about to be.
The man who would be Yugi's Dueling opponent was glaring at him with hard eyes, eyes that rivaled even the most serious Duelist Yugi had ever faced. He was refusing to go anywhere without destroying Pegasus or Dueling for the right to destroy Pegasus, and not even Téa could convince him to do otherwise. So they were stuck Dueling on the front lawn of Industrial Illusions of Japan, which was a notoriously bad Dueling spot.
Yugi didn't mind any of it. He was itching for a good duel, and it had been a full year since he could say he faced a truly challenging opponent. Despite the fact that this man knew as much about Duel Monsters as Joey knew about advanced KaibaCode programming, Yugi had a feeling that he had the skills necessary to pick up the game quickly and play like he'd been Dueling his whole life. He couldn't wait.
Too bad Pegasus had to go and ruin it.
"As much as I love watching two Duelists go mano a mano, it won't be necessary."
"Pegasus?" Joey spat. "What are you saying? You realize this guy wants to kill you, right?"
"I'm aware of his intentions. You can be sure of that," Pegasus said. He placed a hand on Yugi's shoulder and shoved him aside. Yugi would have fallen against one of the creepy, toon-shaped hedges if Joey hadn't reached out and caught him in time. Pegasus continued as if nothing had happened. "But he's right. I am supposed to die."
Téa crossed her arms. "That's crazy! You can't expect us to believe you want to die, Pegasus! You're way too vain for that."
"Vain as I am, I can't deny that this man–what was your name again? Nigeria?–is correct."
"That I am. And it's Migeira."
"Right. Migerio." Pegasus placed a forlorn, overly dramatic palm across his forehead. "I saw it all back when I had the Millennium Eye. Alas, it was not I who was meant to live throughout these years. I can't go on knowing that I'm taking the place of some innocent soul."
Although Yugi found it difficult to believe that Pegasus would be so selfless, he realized that there was a very compelling selfish reason that Pegasus might want to die. "It's because of your wife, isn't it?"
Pegasus stopped mid-dramatic gesture, and opened an eye to face Yugi. "You can see right through me, can't you, Yugi-boy?"
Yugi resisted the urge to shrink away from that gaze. "It's plain for all to see. If that's your reason and your willing to sacrifice yourself, I see no reason not to let you go along with your plans."
"Then it's settled," Migeira said. He pointed his revolver-arm at Pegasus. "I suggest you all stand back."
Without even waiting for Yugi and his friends to get completely out of the way, Migeira charged up his attack. They all dove to the ground as a beam of light shot out of the revolver straight for Pegasus, who faced his impending doom with a smile.
"Say goodbye to Kaiba for me," Pegasus shouted as the light swallowed him whole.
"Uh…what just happened?" Tristan asked as a thin dust began to settle around them.
"The true future has been restored," Migeira said. He sounded less like he wanted to kill the nearest person, and the set of his shoulders loosened somewhat. "The soul that left in Pegasus' place has returned to this world."
"Oh yeah?" Joey asked, jumping to his feet. "And just who might this soul be?"
Joey didn't notice that his question went unanswered as Yugi gave what could only be described as a squeak, which was surprising since everyone thought he had moved past that stage in his vocal development. Joey almost gave the same reaction himself when he realized what Yugi was going on about.
In the middle of the front lawn of Industrial Illusions of Japan stood Pharaoh Atem, whose presence hadn't graced the earth in nearly a year. His regalia shone brightly in the light of the afternoon sun, and his existence there was the only proof they had that anything out of the ordinary had happened that day. It was pretty compelling evidence.
"I would ask what was going on," the pharaoh said, his arms folded the way he always used to hold them, "but something tells me you wouldn't be able to tell me if you tried."
Yugi was the first to recover from his shock. He rushed forward to hug his dear friend who he thought he would never meet again in this life. Next was Téa and then Joey and then Tristan, until they were all a crying heap on the front lawn of Industrial Illusions of Japan.
No one noticed a silver streak that looked like half a human body disappearing into a vortex in the sky.
Author's Note: The anime I crossed this over with is Samurai Deeper Kyo! I watched it this past summer with BigBangLuver and Dookaller, and we thought it was hilarious. We were only watching it because it had a lot of the Yu-Gi-Oh! voice actors in it, and even though it was really bad, it was worth it. So worth it. Especially for that ending.
This whole story is based on the fact that Pegasus actually dies in the manga at the end of Duelist Kingdom. I thought it would be funny if Migeira visited the anime world where Pegasus is still alive to try and fix everything, since he's always going on and on about fixing the future. Which is pretty hypocritical for a guy who didn't even show up in the manga.