This has me puzzled for a moment, but the map came to my rescue. He had moved off the platform where he initially stands, to the middle shielded room. I had to use another console to drop the field and reach him- he must have run off to let his creations play.
So I searched every room off to the side...did the 'bypass security' thing..no bad guy
However I left the mission, went on a Patrol Mission, completed that. Then I came back to that system and I had the option to continue. So I continued, and the actual lab part had reset. So I killed all the augmented again, and this time the bad guy was just like you said...off in the room in back behind the security field. Presto done.
Somehoww I think the first time the mission got confused, maybe because I had to respawn or something.