rule interpretation

Question
This happened in a local high school game.......Situation: runner on third, two outs, two strikes on the batter.. runner having a big lead arrived and stepped on the plate before the pitch which is a strike caught by the catcher...will the run count since the runner stepped on the plate before the pitch, or  will rule 4.09(a)exception 1 apply in this situation.. thanks

Answer
The run will not count.

I'll explain the rules using NFHS Rules, as these are the rules used in most states for high school baseball. If the league uses a different rule book, let me know and I'll give you the applicable rules for that ruleset.

Rule 9-1-1 states a run is scored when a runner touches home plate. There are several exceptions, but I'll focus on one: A run is not scored if the runner advances to home plate during action in which the third out is made as follows: (a) by the batter-runner before he touches first base (Rule 9-1-1 Exception (a)).

Rule 8-1-1 states "A batter becomes a runner ... when he is charged with a third strike" (8-1-1b). However, it also states "If third strike is caught, he is out an instant after he becomes a runner."

So, the batter becomes a runner the instant the third strike occurs. If he is then putout (by the catcher gloving the pitch in flight OR by being thrown out at first base if the ball wasn't gloved in flight), he becomes a batter-runner whose third out was made before touching first base. Therefore, because the run scored during this third out action, it does not count.