The timer as it appears in N+.
The timer is a bar at the top of the screen. At the beginning of an episode, the timer starts with 90 seconds and decreases with time. The player can increase the amount of time by collecting gold, with each piece adding two seconds to the timer.
The amount of time the player has at the end of one level carries over to the next level in an episode, meaning you do not start each level with 90 seconds (unless you're doing highscores for individual levels).
If the ninja dies to an enemy or by hitting a surface too hard, the timer resets to the amount it was at the beginning of a level. For example, if you start the level with 120 seconds and you get hit by a Zap drone, you will restart the level with 120 seconds on your timer.