How does the transporter work?
While there is no absolute canonical answer, we can piece one together from various clues, that fits nearly everything seen on-screen, and in the TNG Tech Manual. We have some evidence of the inner workings of transporters, but not much. They employ Heisenberg compensators, pattern buffers, phase transition coils, Biofilters, matter streams, confinement beams, and matter-energy converters, and phased matter. As for what they do, we know that you are conscious during transport (Star Trek II: The Wrath of Khan, “Realm of Fear” [TNG]), but can also be held in stasis (“Day of the Dove” [TOS], “Relics” [TNG]). Further, while in transport, you appear whole to yourself. I hypothesize that the Annular Confinement Beam first locks onto, then disassembles the subject into phased matter, via the phase transition coils, causing it to take on a very energy-like state somewhat akin to plasma, called phased matter. The matter stream is then fed into the pattern buffer, piped through wave-guide condui