I'll keep it simple. Pretend that you're blue:

1) Start the game
2) An arrow will be pointing at the red base. Go there to capture the red flag. Your opponent will most likely go to your base (the blue one) and capture the blue flag
3) The arrow now points to where your own (blue) flag is at the moment. So if the opponent has it, the direction of the arrow will constantly change (if the opponent moves). If you kill your opponent, the blue flag will be returned to the blue base.
4) Score the point by bringing the red flag to the blue base when the blue flag is still there.

If you're red, it's vice versa of course