EMP is the acronym for electromagnetic pulse. It creates an electromagnetic field around itself, which disrupts electronic devices, causing them to shut down within range. All of Zion's hovercraft carry devices capable of producing EMPs. The blast from an EMP is sufficient enough to disable any electrically-powered machine within its blast radius.
In the initial years of the Machine War stationairy EMP cannons alongside EMP cannon equipped human tanks capable of mass destruction and deactivation against the Machines, however the latters numerical advantage would mostly nullify this threat. EMPs were also used against the Machines by the hovercraft crews of Zion as their only real way of combatting them. When Smith entered the Real World disguised as Bane, he uses an EMP to take out most of the hovercraft, leaving only the Nebuchadnezzar, the Mjolnir, the Logos, and the Vigilant operative. During the Battle of Zion, the Mjolnir, under heavy attack from Sentinels manages to burst into the Dock and activate its EMP, crippling the Machines army of Sentinels and its digger machines. The victory is short-lived, however, as Zion's defenses are also rendered inoperative and a new swarm of Sentinels arrives for the final assault.