Flee means just that - when your unit sees the enemy thundering down upon them, they turn tail and run! This is a rather desperate option as once troops begin to run they tend to carry on going, and may run away from the battlefield altogether, whether you want them to or not.
Units that have declared a flee reaction will flee in the compulsory moves part of the movement phase, (in the same order as the charges were declared).
Fleeing is done by first pivoting the units on the spot (around their centre) to face directly away from the charging enemy, and then moving them directly away from the charging enemy unit by 2D6" if their Movement characteristic is 6" or less, or by 3D6" if their Move is more than 6".
If a unit is fleeing from two or more different chargers, they will flee directly away from the enemy unit with the highest unit strength (roll a dice in the case of equal unit strengths).