You traveled to this facility and battled an agent called Reinhard. He boasted that the Council's new Mekmen were more powerful than you could dream. You journeyed to another Council base, where you recovered physical evidence of these new Mekmen for Citadel to analyze.
When the technology foiled Citadel's scans, he sent you to Fareed Abdullah for an expert opinion. The Council and Fareed revealed the terrible truth at virtually the same time. The Mekmen were being created from the same technology that built Citadel!
After consulting with Manticore, Citadel sent you to a mekman manufacturing facility, which you shut down.
Showing as much emotion as anyone has ever seen from him, Citadel sent you to interrogate the Council soldiers in Independence Port. You took to the streets, and returned with a data disc bearing the locations of three Mekman production plants.
You shut them down one by one. At the last facility, you discovered the identity of the mastermind behind these advanced Mekmen. It was none other than Vandal, the Council's own twisted genius.
You traveled to Vandal's lair and defeated him, likely freeing Citadel from a terrible legacy.