Board Thread:Theories and Speculation/@comment-44142243-20200416151624/@comment-4912646-20200417090001

The series arguably doesn't actually explain how the Mangekyō works aside from how to awaken it and the requirement for using Susanoo. For example, there isn't even any dialogue that says "each eye gains a single technique that's different for each person", it's just something we've picked up on through observation. Sort of like how people now theorize that each set of Rinnegan grants a unique ability to their owner, but there's less evidence to go off of for that. Back in the day, it was actually common belief among fans that every pair of Mangekyō could automatically use Tsukuyomi and Amaterasu, whereas techniques like Kakashi's Kamui had to be gained through training, but that obviously didn't turn out right.

That said, I think Tobirama's explanation of how the (regular) Sharingan awakens in chapter 619 gives us a pretty good indication of how this all works: under certain circumstances, the Uchiha's brain releases special chakra that permanently transforms the eye, even if it's later removed from their head. Awakening the Mangekyō is likely caused by a similar reaction, so it would make sense that creating the EMS works the same way, effectively "overwriting" the eye's existing properties with new brain chakra, while still retaining its "ocular power" (indicated by the two patterns overlapping).

The real question is whether an Uchiha could awaken a new set of Sharingan or Mangekyō by transplanting another's eyes, or if each stage of activation can only happen once per person.