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I was reading this answer and it got me thinking, how can Sasuke obtain the EMS, if Itachi's eyes were in worse condition than his? Itachi's eyes were losing their light they weren't in "good" state to be considered a good replacement. How did they heal when transplanted?

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Firstly, by attaining the Eternal Mangekyō Sharingan through transplantation of eyes (of a blood relative, ideally a sibling's), the following upgrades are received by the user:

  • Deteriorating vision is restored.
  • Their Mangekyō-based abilities are made stronger and they no longer suffer any negative side-effects from the usage.
  • The user will retain all their previous techniques from their original eyes.
  • The user will be able to access the Mangekyō abilities of the donor.

So what basically happens is that, the eyes taken from a sibling get a new host and whatever drastic conditions (related to vision) the donor had gone through while they had the eyes, doesn't affect the new host.

In Sasuke's case, his vision was deteriorating, so he decided to transplant his brother's eyes, which were in a similar condition. When the transplantation is completed, he is able to see clearly and moreover, get an increase in his dojutsu skills. This clearly proves that the precious condition of the eyes doesn't reflect to the new owner. There is no other case to prove otherwise.

Reference: http://naruto.wikia.com/wiki/Mangekyō_Sharingan

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