Before getting into the answer of “How Did Madara Get The Rinnegan” in detail, we’ll deal with the short answer first
Madara had both Asura Otsutsuki and Indra Otsutsuki’s chakras which led to Rinnegan’s awakening.
To get into the long answer, we first need to correct common misconceptions:
Rinnegan isn’t an evolution of the Sharingan, it is more of a sibling dojutsu (like both’s relation with the Byakugan).
In other words, while the Rinnegan, the Sharingan, and the Byakugan have similar origins (i.e., Kaguya), they were separated from each), they aren’t linked to each other like, say, the Sharingan and the Mangekyo Sharingan.
Hagoromo states that to obtain it, one must have Hagoromo’s chakra, obtained by having both Asura and Indra’s chakra.
Ergo, Kabuto’s hypothesis on how to get the Rinnegan (Senju & Uchiha chakra + Sharingan)…
… Is not entirely true. For example, if Asura’s reincarnate managed to obtain Indra’s chakra in some way or form, he’d eventually awaken the Rinnegan as well.
With these elements in mind, the Rinnegan is extremely rare, and Black Zetsu notes that even when he tried to manipulate previous Indra and Asura reincarnates, he was unable to make them awaken the Rinnegan.
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With these elements in mind, getting the Rinnegan, no matter how, tends to be a feat in itself, especially regarding Madara.
In the latter’s case, the legendary Uchiha fought Hashirama and bit off his flesh as well as his chakra.
Since Hashirama and Madara are respectively Asura and Indra’s reincarnates, this means Madara had already filled the initial requirements to obtain the Rinnegan.
After spitting the flesh he bit off from Hashirama, he implanted it — and the chakra that comes with it — on himself.
This led to Madara gaining the Rinnegan in his old age. However, since he was nearing too old to go on with the Eye of the Moon plan by himself, he gave the Rinnegan to Nagato when the latter was still a child, with no one noticing him.
Aware of his own mortality, Madara planned to have Nagato resurrect him with the Rinne Tensei once his Eye of the Moon Plan was nearing completion.
By the time Madara trained Obito and died, he no longer had the Rinnegan. However, he regained it thanks to Kabuto when the latter resurrected him with Edo Tensei.
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Kabuto implanted Hashirama cells into Madara, leading the latter to regain what seemed to be a limited form of the Rinnegan.
As in, despite having the Rinnegan himself, Madara still needed an alive Rinnegan wielder (Obito by the time of his resurrection through Edo Tensei) to resurrect him with the Rinne Tensei.
Upon his resurrection in flesh and blood — thanks to a Black Zetsu-controlled Obito —, Madara lost the Rinnegan Kabuto made him, due to these eyes being, essentially, « fake ».
However, he regained his very first Rinnegan eye thanks to a White Zetsu who found it: Obito, unable to wield both Rinnegan eyes, had hidden it for safekeeping.
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During that same occasion, he also cut off the arm of the Zetsu who gave him back his Rinnegan eye: he had lost his own arm previously and grafted the severed Zetsu arm to himself to make up for that loss.
He regained his second Rinnegan eye through a complex process: he first stole Kakashi’s Sharingan to gain the ability to use Kamui.
From then, he could enter the Kamui dimension where Sakura and Obito had just saved Naruto’s life. However, Sakura was unable to destroy Obito’s Rinnegan as the latter requested before Madara arrived.
Madara killed two birds with one stone, not only he had Black Zetsu re-possess Obito — since the latter had previously overpowered his control to help the Shinobi Alliance — but he regained his Rinnegan and gave back to Obito Kakashi’s death.
Unlike previous times, Madara didn’t lose his Rinnegan from then, keeping it up from then to his final death.
What happened from then on is unclear, though headcanons have been made about their fate, some think they’ve been kept around as spare eyes, others believe that they were destroyed due to their overwhelming power which made them too powerful in the long run.
Hope it helps.
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