The EMP can be discharged by using the Power Switch and turning it upwards. This will result in an electric shock happening outside the submarine in a large radius. The electric shock will do a large amount of damage to any enemies caught in it. This will also cut off all power to the sub for a short time. The EMP starts charged and recharges over time after being used. The progress can be seen in the three blue bars located on the Power Switch.
The EMP damage is calculated by the following equation: (5 + Amount of EMP Upgrades) damage per 0.3 seconds