When a driver has severely violated the rules of NASCAR or is driving in a manner which creates a threat to other drivers and even fans at the track, they will be "black flagged" or pulled from the race and not allowed to return to the track. A driver can also be black flagged if the car itself is somehow posing a danger to the other drivers although usually a driver will leave the field prior to that on advice from his crew.
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When NASCAR waves the black flag directed towards a certain driver during the race, it signals to that driver to come into the pits. There are several reasons, it could be for not maintaining minimum speed, damage on the car such as a loose hood or dragging parts or even for disobeying the rules (pit road speeding etc.)
As long as the driver pits and fixes the problem or serves the penalty, NASCAR will allow them to continue racing. If the driver fails to come in, their laps will no longer be scored.
Nascar has flags that are used to notify a driver of track occurrences during a race.
The checkered flag is used to indicate the end of a session, whether it be a practice run, qualifying or the actual race. It originated in the early 1900's.