the red one
This could refer to anger, someone wearing red. Or an enemy.

looking for the blue one
This could refer to sadness, someone wearing blue. Or an allie.

taken by the black one
This could refer to Squall, or someone who wears black.

Overall, this could relate to Galbadia Garden (red) searching for Balamb Garden (blue), B. Garden is now commanded by Squall (black.