protagonist of the matrix crossword clue

 The answer to the crossword clue "protagonist of the Matrix" is NEO. It is a 3-letter word.

Neo is the main character of the Matrix film trilogy. He is a computer hacker who learns that the world he lives in is actually a computer simulation created by machines. He teams up with a group of rebels to fight against the machines and free humanity.

The name "Neo" is a reference to the Greek word "neos", which means "new". This is a fitting name for Neo, as he is a new kind of hero who is willing to question the reality he lives in and fight for what he believes in.