Raid the Nemesis automaton research lab and figure out what they've been working on
Nemesis likes to get top talent wherever he can find it, and he doesn't mind taking people from other organisations. I've been looking through the records you found, and noticed that he made a big push on hiring ex-Council members a few years back. Those men were all asigned to part of Nemesis' automaton fabrication division, and I think they're still working there. They're all wanted men, and that's a good enough excuse to send you in there to raid the automaton research lab and figure out what they've been working on. This is a hunch, but I have a feeling that could be a very interesting place.
Defeating the men in there is fine, but the real goal for us is to find out what they're working on. I have to wonder why Nemesis transferred those ex-Council guys to his automaton group? All of Nemesis' desgins are originals using his own technology, so it's unlikely that he was hiring them to improve his own automatons with Council designs. They'd be completely incompatible. It's a mystery.
Laboratory @ Perez Park (Nemesis,Council)
This smallish lab has been hidden underground, but it seems to be well-equipped with Nemesis-designed robotics gear.
Objective: You found a disassembled vampyr automaton!
Mission Complete: You found evidence that Nemesis has infiltrated the Council with automatons!
Vampyr imposters? I gotta admit, I admire his guts sometimes. Only Nemesis would be that bold. It makes sense, though. Normal troops go through so much mental and physical indoctrination and examination that an automaton would get caught, and Council robots are so different from Nemesis' technology that it would be easy to tell an imposter.
It's kind of funny, but it still has to be stopped. If Nemesis could subvert a big enough portion of the Council, it could be a disaster. I need you to take out one of these imposters right in a Council base, where all the troops can see it. You'll also need to take out the rest of the command staff just to make it look normal, but I'm confident you can handle that. Don't worry that we're helping the Council, either. They'll have to spend so much time testing all of their vampyri, this will derail their operations for months.
This Council base is being run beyond even the Council's normal standards of efficiency.
Mission Complete: You defeated the Vampyr automaton, revealing its presence.
We knew that Nemesis used his automaton imposters to take over business, run front companies, and spread confusion during disasters. But I guess no one ever though about him using the automatons against rival villain groups. Really, it makes sense, though. As far as Nemesis is concerned, everyone is just a tool to be used in his bid for power.