Just to make a point about digitalizing humans.

When the laser hits/zaps the subject "Kevin Flynn", his moleculas are disassembled and kept "in the range" of the laser itself for an undetermined amount of time. In the while, the computer has scanned the structure of Kevin Flynn and thus generates a detailed informatic "model" to recompose his body (remember: the purpose is teleportation). A kind of program to reproduce/mold Kevin Flynn from head to foot, particle by particle.

Indeed, THAT model/proxy is FLYNN, the program of Kevin Flynn. FLYNN keeps the consciousness of Kevin Flynn "intact" because Kevin's neural patterns are reproduced into him and his own "head" made of source code.

Basically, both Kevin Flynn and Sam Flynn become "programs of themselves". They are not themselves and they are themselves AT THE VERY SAME.
GENIUS!

So basically, we got:

Original human Kevin Flynn
FLYNN (TRON 1)
Second human Kevin Flynn (TRON 1's ending/LEGACY's 1989 era)
FLYNN 2.0 (TRON LEGACY)
Third Kevin Flynn ???

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