You'll notice a meter at the bottom of the radar appears when ALERT is initiated. To get out of ALERT mode, Snake will need to stay hidden from the enemy's direct view for approximately five seconds.
This is the last mode you want to be in, but is the only mode that will occur right out of NORMAL. Once ALERT is initiated, the normal guards will call for back-up attack units, and together they will hunt Snake down. When an enemy or camera plainly spots Snake they will initiate ALERT mode. By default, the game is in NORMAL mode and it is definitely the mode you want to be in while playing Twin Snakes. In this mode, the enemy soldiers will patrol as usual, following their scripted routes with the typical alertness.
When Snake is sneaking through the game and the enemies have no clue about Snake's presence, the radar is in NORMAL mode.