After battles with Aoshi and Soujirou, Kenshin, a bit beaten up, entered the final battle to decide the fate of Japan with Shishio Makoto. Shishio's special Big Burning Room at the top of his base was the location. The two powers clashed and it was Kenshin who was knocked back. Rebounding, Kenshin leapt up and slammed his sword down on Shishio, who had blocked. The power from the impact was tremendous, it pushed Shishio into the floor a bit, but again, the two found their swords connected to each other. Shishio decided to use his first technique here. Lighting his sword on fire, using Kenshin's Sakabatou, Shishio hit Kenshin with his Homura Dama.

Kenshin was cut and burnt slightly. Following up, Kenshin executed the Ryu Sho Sen. Because Shishio had seen the technique from Kenshin's fight with Senkaku at the Shingetsu Village Inn, he was able to easily catch Kenshin's sword before it touched him. Shishio then placed his hand over Kenshin's face and took a bite out of his neck. That had stunned Kenshin for a bit, but when he got up, Shishio and him discussed their goals. Neither had seemed to agree with one another, thus, the fight resumed. Shishio had surprised Kenshin. Using his Homura Dama technique, Shishio created a wall of fire around his opponent. Out from the flames came Shishio's hand to grab Kenshin by the neck.

There was no escape from Shishio's grasp. Kenshin was helpless was Shishio igniting his sword and cut his gunpowder soaked glove. An explosion, Shishio's Guren Kaina technique, had sent Kenshin flying. Kenshin was knocked unconscious from the attack. Just when things were looking bad for Sanosuke, all alone on Kenshin's side, the doors to the arena were broken through. Saitou had made a grand entrance with his Gatotsu aimed for the head of Shishio. Once it connected, Saitou put a grin on his face. However, that grin soon disappeared. Shishio had an iron bandanna equipped.

Saitou wasn't fighting to help Kenshin; he was fighting for his own sense of justice. Once again, Saitou executed his Gatotsu, but Shishio caught his blade after learning the frequently used technique. Deciding to change things, Saitou used his Gatotsu's second stance. Shishio avoided that by using his Homura Dama to create a wall of fire. The distraction allowed Shishio to leap away into the air, but Saitou followed up with an anti-air Gatotsu just as Shishio was coming down with his Mugen Jin. When both had landed on their feet, it was Saitou who was hurt. Yet, Shishio had his back turned to the Miburo. Without wasting time, Saitou executed his Zero Gatotsu.

Surprisingly, Shishio was able to block the zero stance Gatotsu. With his hand near Saitou's open wound in his chest, Shishio touched his gunpowder soaked glove with his burning Mugen Jin. Saitou was thrown back from the Guren Kaina's explosion. The same technique had knocked both Kenshin and Saitou out. Enraged, Sanosuke charged into battle, ignoring Kenshin's request of not interfering. Sanosuke's first punch was avoided, but his second was caught. Shishio squeezed Sanosuke's fist until he punched him away in the gut.

Somehow, Sanosuke was able to find an opening in his second charge towards Shishio. The Futae no Kiwami was hit accurately on Shishio's cheek, but also broke Sanosuke's fist. Yet, the move barely grazed Shishio. A bit annoyed by Sanosuke, Shishio rocked him with a powerful punch, sending the ex-gangster crashing into a wall. Victory was on the mind of Shishio. He had defeated all of his opponents and began celebrating with a lengthy evil laugh. However, there was one man left for him to face. Aoshi stepped onto the battlefield to stall time for Kenshin to recover. Their alliance, short as it was, had been broken.

Aoshi faded away, using his Ryuusui no Ugoki. Shishio would not be tricked by what he considered a slow technique. Shishio's Mugen Jin and Aoshi's twin kodachis clashed a few times. Once separated from Shishio, Aoshi crossed his swords and ran forward, prepared to execute the Gokou Juuji. Shishio saw the move coming, so he easily blocked and thrusted the butt of his sword into Aoshi's throat. Aoshi was up against a wall and Shishio attempted to strike him with his Homura Dama. With whatever strength he had left, Aoshi managed to leap behind Shishio. Again, Shishio cockily left himself open for an attack. Aoshi hesitated before turning his kodachis upside-down.

As predicted, Aoshi used his Kaiten Kenbu Rokuren. Again, Shishio surprised someone when he blocked their most powerful move. Aoshi had lost his one of his kodachis and was knocked back by Shishio's Homura Dama, but that's when the wind started to grow heavy and leaves began to circle around the arena. Kenshin was revived, and so were Saitou and Sanosuke. Shishio liked the challenge, but Yumi was concerned about her lover fighting for over fifteen minutes by then. Kenshin and Shishio clashed once again. Unfortunately, the same event was repeating itself. Kenshin got his neck caught by Shishio's hand.

Thoughts ran wild in Kenshin's mind. He had a goal, and that was to return to the ones he loved. With a newfound determination, Kenshin broke out of Shishio's grasp, causing his own attack to explode in his own face. A five hit combination was then executed by Kenshin - Ryu Tsui Sen, Ryu Sho Sen, Ryu Kan Sen Kogarashi, Ryu Kan Sen Tsumuji, and Ryu Kan Sen Arashi. All five were consecutively hit. Shishio had barely blocked all five attacks. Still, Kenshin's deadly combination had not knocked Shishio off of his feet. Shishio decided to hit Kenshin with an attack of his own. The Homura Dama was executed, yet, that had no affect on Kenshin. His body was no longer affected by it.

Quickly, Kenshin performed the Kuzu Ryu Sen. The final blow of the nine hits was at Shishio's head. Shishio was thrown back from the power of the technique and was temporarily knocked out. As Kenshin caught his breath, the flames around the arena began to scream. Like how the wind and leaves reacted to Kenshin's warrior spirits, the flames were reacting to Shishio's. Shishio had been revived just like Kenshin. There was only one round left in the battle and the only way to decide who'd be the winner was with the succession techniques of both men.

Kenshin had executed his Ama Kakeru Ryuu no Hirameki once both he and Shishio were prepared. Somehow, Shishio blocked the Hiten Mitsurugi Ryuu succession technique. With his Mugen Jin, Shishio ignited it by sparking it on his scabbard. A tornado of fire known as Shishio's Kaguzuchi succession technique circled around the Mugen Jin. However, a mysterious void opened up and began sucking Shishio closer to Kenshin. The Ama Kakeru Ryuu no Hirameki had created the abyss. There was no escape for Shishio, he was struck with a powerful Ama Kakeru Ryuu no Hirameki. When he got up, however, Shishio began furiously scratching his body.

Because he had an abnormal body temperature and surpassed his limits, Shishio was burning up. Yumi had run into the battlefield and asked for Kenshin to discontinue the fight. Kenshin lowered his Sakabatou in respect of Yumi's request, but Shishio took advantage of the situation. He stabbed Kenshin in the side and also stabbed Yumi in the process. Yumi had found happiness in death, as she had finally assisted Shishio once in battle. Kenshin found no reason for happiness in such a predicament. With Yumi's death, Shishio had somehow summoned up even more power, the last of whatever he had left.

Shishio had far surpassed his own limits. His body temperature was boiling as his own blood evaporated. The wound in his side had Kenshin kneeling on the ground. When Shishio struck down, all Kenshin could do was helplessly block. Shishio's power was great, so great that even Kenshin thought for a second he might lose. However, Kenshin had the determination to live. As the floor began to break apart, Shishio suddenly stopped pushing Kenshin down. For the second time, Shishio began scratching his body intensely. Finally, he combusted into flames. The flames of Hell inside of him finally took his life. Kenshin had won the ultimate battle.