There's actually a lot of instances where you can see how members of a villain group are created.
Irradiates: Gallant Major Gertz and his Courageous Crew, Desert Crisis - you watch as Major Gertz, sent to scout into the irradiated caverns where Gigaton is hiding, goes mad from radiation poisoning and begins worshipping Gigaton, taking the first step to becoming an Irradiate. Later on, you'll see him in his hideout in the spire above the Deranged PRIMUS camp, having fully turned.
Sovereign Sons Zombies: A mission in Vibora Bay has you exhuming recently-buried 'zombies' and giving them an antidote to return them to normal and ensure that the Sovereign Sons cannot use them.
Nephilim: Created by the sacrifice of a living person by the Trey Kings.
P.S.I.: Recruited from ordinary citizens with latent psychic potential through their front organization, Mind Inc. You can meet the recruiters yourself in one of the missions from that mind-controlled cop that keeps complaining of headaches. Later on, you'll need to collect mind control devices from them, and disable psychic somnabulators designed to manipulate the dreams of sleeping people.
