The only ability of the Rinnegan that could affect Chojusen was the Deva path's gravity manipulation. However, Madara's Eternal Mangekyo Sharingan's special ability was actually related to time. Madara could slow down time to half speed for him and because it was an eye ability of the Eternal Mangekyo, he could have it constantly activated! If Chojusen knew, he would curse the creator of these eye abilities that got more and more absurd as time progressed.
The Asura Path's mechanized transformations were a joke compared to Chojusen's base body's strength, a statement that also applied to the Animal Paths' summoning technique. The Human Path would not work on Chojusen as he had Immortal Rank Yin, Yang, and Chaos Law Principles. Chojusen's Immortal Rank Energy manipulation made the Preta Path's ability to absorb his energy void and the Naraka Path… well, it would be less than unlikely that Chojusen allowed himself to get caught, and its restoration ability would not be usable to Madara as he had yet to establish his six paths in other bodies.
Additionally, since the Rinnegans were Madara's to begin with, he didn't have to wait for a five second cool down like Pain every time he wanted to use gravitational manipulation. Madara disregarded the consequences and activated all of his most insane abilities at the same time. He was clad in a complete Susanoo with nine Truth Seeking Orbs revolving behind his back, he flipping the gravity Chojusen experienced every couple milliseconds, he moved and perceived time twice as fast, and his four limbo clones were supporting him on top of all the other abilities.
One clone started calling more meteors to the ground, another clone blasted Chojusen with Fire Release Attacks, yet another clone used Storm Release attacks, and the last clone surprisingly started using Wood Release.
Chojusen's used the first stage's application of his Fiendgod eyes to the best of his abilities and summoned Elemental Sage Clones as support. A Water Elemental Sage Clone countered Madara's Fire Release using Limbo Clone, A Wind Elemental Sage Clone did the same for the Limbo Clone that used Storm Release. A Fire Elemental Sage Clone kept the Wood Release using Limbo clone busy. Last but not least, a Lightning Elemental Sage Clone blasted the meteors of the remaining Limbo Clone.
Chojusen's true body expanded with the Multisize technique's application once again, and he personally dealt with the Susanoo clad Madara. His body and staff also received a generous application of his Elemental Coating technique; coated with lightning energy, of course. This time the two of them were moving much faster and more erratically. Every clash between Chojusen's giant staff and the Susanoo's sword resulted in quakes, both in the air and on the ground. The landscape was raised and thunder echoed from above.
Every so often, the remnants of the battling clones would graze by the main bodies fights. Water Bullets that weren't canceled out by the Fire Release Limbo clone would spawn titanic Tsunamis, Flame Bullets would char the ground black, Lightning Javelins would penetrate the ground and explode from within, and Wind Blades would periodically cut through the world like it was butter.
Madara's Wood Release would leave behind a trail of broken and burned wood even though there were no trees for hundreds of kilometers. Boulders and Lightning rained down from the sky from the confrontation of Chojusen's Lightning Clone and the meteor summoning Limbo Clone.
The only reason Chojusen didn't end the fight immediately by going into Fiendgod Butterfly Sage Mode was because he felt that if he kept fighting against all this space and time abilities of Madara's true body, he could perfect his space and time law principles; he was already reaching the point of being able to see a bit through the limbo dimension.
Chojusen could also see his progress with space and time improve as his eyes improved ever so slightly as the fight went on and his space locking and gravity skills started to make an impact when he fought with Madara's true body.
When the feeling of a complete breakthrough manifested in his body, he noticed that his teleportation could now work against Madara's domain; the Rinnegan. He could also see the Limbo clones as plain as day. So he resolved to end the fight with the most spectacular of his abilities.
Now that Chojusen could see the Limbo Clones, he used his Dimensional Seal on some rocks and sealed the clones away after a burst of teleportation. When his space and time law principles of dimensions was mastered, his dimensional seal improved to the point where he could now seal away peak-tier Demi-Immortals. Madara's true body was well above the full Immortal Rank, but Clones could only be so strong, and his were just high-tier Demi-Immortals.
Chojusen then took a second to shoot a flame bullet into the sky and create a horrifying storm of lightning and fire law principles. Madara was shocked, but he fought Chojusen in an attempt to stop him from completing whatever attack he was planning. Unfortunately, his efforts yielded no return as Chojusen could just teleport away from him or use his Void Cloak to become intangible. Now that his space law principle of dimension was mastered, he could sleep around Madara and nothing would happen.
As Chojusen avoided Madara's attacks and waited for his fire and thunder storm to charge up, he noticed that the people in his personal dimension were quite riled up. It seems that the jinchurikis recognized Madara and spilled the beans. Now all the powerhouses in Chojusen's personal dimension wanted to come out to help Chojusen; they didn't think Chojusen had the power to mess with a Tail-Beast infused Madara.
Chojusen had one of his clones calm them down. But it was only after he promised that he would release all of them when the fight was over, that the rowdy crown stopped their protesting.
Back in outside world, Chojusen looked at the sky and smiled as he noticed that his preparations were complete. The battlefield was now being recklessly ravaged by the wild thunder of the law principles Chojusen summoned, until Chojusen stretched out his hand and beckoned the thunder to form a ball in his hand.
The moment Madara saw the ball of lightning in Chojusen's hand, he left the site of battle; augmenting his speed to its absolute max. He knew that the ball of thunder was just as powerful as Chojusen's supernova, or maybe even stronger.
Chojusen didn't mind Madara leaving. He calmly created a supernova in his other hand and then teleported away. By now Madara was hundreds of kilometers away from their battlefield, but Chojusen appear right in front of him with no problems. Madara could feel his death approach as he watched Chojusen shove his Supernova into his Lightning Field.
Just before the two finisher attacks collided with each other, Chojusen teleported away. Madara did everything in his power to survive the attack. He brought out a complete Susanoo, he covered his body with all his Truth Seeking Orbs, his limbo clones further shielded him, and all of this was covered by an endless mass of wood clones.
As Chojusen's attacks finally made contact, the world ending scene Madara was expecting didn't come immediately. The world first went quiet, and all its colors faded into a monochrome scheme. Then a blinding flash of light escaped from the epicenter of the attack; the light could even be seen hundreds of thousands of kilometers away. The entire world shook slightly and everything within a hundred kilometers of collision site stopped existing.
White-hot flames and purple thunder then went on to consume everything for the next four hundred kilometers. Chojusen watched the whole event a couple dozen kilometers above the earth's surface. He thought he went a bit overboard when he saw that the ground caved in to the point where lava and magma was visible.
His attention was then drawn to a crippled Madara, barely standing with his remaining leg on one of his Truth Seeking Orbs. He was floating in the air a couple hundred feet away from where the chaos caused from Chojusen's attack stopped.
Chojusen said "Wow, I can't believe you survived that. No one has ever pushed me this far..."
"You think you've won?"
"What could you possibly do now that could threaten me? You are barely even alive."
Madara snorted at Chojusen's words and looked at the moon. He said "Infinite Tsukuyomi."
Chojusen followed Madara's sight and found that the moon turned red and had the pattern of a hybrid between the Sharingan and the Rinnegan. "A genjutsu? After all the fighting we've done, you think I'll lose to you with regards to yin manipulation?"
Chojusen didn't want to bother with Madara anymore so he shattered his chakra network with a couple staff strikes. Right now, he couldn't kill him or the Ten-Tails would be unleashed and he would have to find another place to seal it away.
Chojusen brought out the people in his personal dimension, now that the threat was gone. He didn't forget to revert back to his regular form so as to not shock everyone by looking like a god ready for battle. However, he forgot where he was and the people that left his personal dimension were shocked more than they would have been from seeing his Elemental Sage Mode, because of the sight of destruction before them.
The final attack caved in the ground for hundreds of kilometers, so even the "unimportant" Jonin level ninjas could see most of the damage the poor ground had suffered. It didn't take long for people to recognize the anomaly that was Madara in his Ten-Tails Jinchuriki form; he was the only pale white thing for hundreds of kilometers.
Hashirama looked at the fallen body of Madara and sighed. He said "Old friend… Why did it have to be this way."
Chojusen said "This was what he chose to do. We can hope for a better future after learning from this experience."
"Right… Still, I can't imagine how powerful you must be to cause this much destruction..."
"Like I said, I'm just an Immortal."
"I see… Well where are we anyways? All I can see is destruction on my left and an endless forest on my right."
"Before our "fight" I had to move him over to a place very far from the village. Otherwise, our attacks might have accidentally destroyed the village."
As Chojusen and Hashirama were talking, a shadow went unnoticed over to Madara's side. Of course, Chojusen noticed this, but a system prompt stopped him from acting.
[Final Mission Alert~
Chain Mission
Stop the allied army. Rewards: 50,000 shop points✔
Stop the new enemies. Rewards: 100,000 shop points✔
Defeat Pain. Rewards: 250,000 shop points✔
Defeat Madara. Rewards: 1,000,000 shop points✔
Defeat Kaguya. Rewards: 5,000,000 shop points + Bonus (Depends on how many steps host completes.)]
[Final Bonus Mission
Bonus Mission E): Seal Kaguya away with the power of a Six Paths Sage. Reward: Will improve the Bonus after the Chain Mission Ends.]
"System… What is a Six Paths Sage?"
[That's a special Sage Mode — kinda like your Fiendgod Butterfly Sage Mode — where the Sage has the powers of the Sage of Six Paths. Lets see… right now you could use your Yang Rebirth on Hashirama, Naruto, or Sasuke to forcefully awaken their innate Sage of Six Paths chakra.]
"Wait, why are they the only people that have the special Six Paths energy?"
[Well they aren't the only ones. These are just the people I think will be able to help you the most.]
The ship of ridiculousness has set sail; there is no going back now...