Endo was only seen patrolling the area or holding some of the workers hostage, guarding them to prvent them from escaping.
He didn't make a notible appearance until two of Cole's mercenaries, Tchen and Toni, went missing. While searching the corridors filled with steam pipes, Endo thought he found the intruder stowed away in one of the closets. Endo took out his gun and fired at it erratically, unaware that Tchen was inside and not the intruder.
Endo (in a somewhat comical state) told Cole that he killed Tchen...just before Sydney appeared from behind and attacked him, knocking him out.