When a baserunner is hit by a thrown ball, the ball is in play. The one exception is if the baserunner is called out for interfering with the throw. The most common such is when a baserunner runs in fair territory towards first base, and gets hit by a throw. In that case the runner is out, the ball is dead, and all other runners must return to their previous bases. Hall of Fame pitcher Tom Seaver once said that if when a pitcher fields a bunt he sees the runner running in fair territory, he should throw the ball into that player's back, getting the out and preventing anybody from advancing on the attempted sacrifice. A batter running to first should run in foul territory, otherwise he risks getting called out if he's hit by a throw. Another case of interference is if the baserunner is deemed to have intentionally moved into the throw. In a famous case from the 1978 World Series, Yankee great Reggie Jackson was forced out at second and then was hit by the throw to first. The Dodgers argued that Jackson deliberately swung his hip into the ball. Certainly Jackson made no effort to avoid the throw. However interference was not called, so Jackson successfully broke up the double play. Runners going from first to second on ground balls to first often attempt to run into the path the first baseman would use to throw to second. Chase Utley did this successfully in an April 2008 game against the Mets. First baseman Carlos Delgado's throw hit Utley in the back (Delgado was charged with a throwing error), all runners were safe, and the play ultimately led to the Phillies' victory.
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If a batted ball hits a baserunner in fair territory, the baserunner is out and the batter is awarded first base. If the baserunner is in foul territory and is hit by a batted ball it is just a foul ball. If a baserunner is hit by a thrown ball the ball is still in play, unless it is determined that the baserunner purposely moved into the path of the thrown ball, or is running out of the base path, then the baserunner is out for interference.
Unless the runner intentionally intefered with the incoming throw, he is not out and the play remains live.
If a batted ball hits a runner, the ball is dead. The runner is out and any other runners return to the base they started on. The batter must re-bat.
Nothing, as long as the runner is touching the base. A runner is out only if touched by a batted ball that is still in play if he is off the base.
If the batter was in the batter's box and did not make an intentional motion with the bat to block the catcher then nothing happens. The ball is still live and in play