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A lot of people overlook the fact that the sage's elder son was blessed with powerful chakra's as well as spiritual energy (not the same thing) and just write it all off as strong yin chakra. So thinking of these to gifts of the Sage as two different things these are a few short theories that I came up with.

Magenkyou:
- The The spiritual energy of an Uchiha is located in the eyes. This spiritual energy activates the special chakras that reside in an Uchiha's brain
- The spirit of the Uchiha is what decides the technique he will gain from awakening the magenkyou
- The reason for magenkyou techniques causing macular degeneration is because they lack the spiritual energy to withstand the technique, therefore the excess recoil gets sent through the eyes and eventually causes the user to go blind
- MS users only have half of the required spiritual energy to affectively use MS techniques the without recoil so they can enhance their body with senju DNA in order to strengthen their body to withstand the strain.
- When an MS user transplants his brother's eyes to gain EMS they do not gain their brother's chakra, however they do gain their brother's spiritual energy that was stored in their brother's eyes in addition to their own.
- The great increase in spiritual energy causes the special chakras inside the EMS user's brain to produce more chakra, possibly equivalent to the increase in spiritual energy.
- Magenkyou Techniques no longer cause recoil because of the needed increase in spiritual energy
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