Someone correct me if I'm wrong, it's rather late =P
The Engineers are like an organic supercomputer, and after being in the SI's core for a while, the Engineer had downloaded/absorbed vital information that the SI collected. And in doing so, I think the Engineer may have downloaded Vergil the subroutine, thus making the Engineer's tag "VRGL."
Also, the cop who betrays you, that you met on the 8th level of the Data Hive, yells for Vergil to open the data stack and let him below. This could could mean a few things.
The cop and Kinsler became aware of Vergil and wanted to acquire him.
Or, the only other one I can think of at the moment, the cop knew Vergil was there all along, and perhaps wanted something else in the Data Hive.