A Crack in Time
Originally and primarily manufactured in the Tombli Outpost on planet Zanifar, they would become the Doctor's new soldiers, also serving under his allies; Lord Vorselon on his warship and Pollyx in his corporate HQ, respectively.
Upgraded elite variants of the Nefarious Troopers called the Chronoguard began to appear late in Nefarious' campaign, first being encountered by Ratchet when he arrived on Vorselon's Warship in order to save Alister Azimuth. They had a blue color scheme instead of red, and had stronger armor. The name 'Chrono' seemed to imply that the doctor would use them in his final occupation of the Great Clock.
Like most of Dr. Nefarious's creations (such as Klunk or the Hypersonic Brainwave Scrambler), they shared at least one quality with their creator; in this case, a visible cranium covered by green glass, referring to organic life forms as "squishies" and saying the word "annihilate" frequently.
Behind the scenes
According to the Insomniac Museum, they were based on robots from science fiction B-movies. In concept art they were given the name of Nefarious Minions. There was a mini-game in the Insomniac Museum that allowed players to design their own pair of Agorian soldiers and pit them against up to 4 waves of Nefarious Troopers, starting out with standard units and ending with a Protomantis in the final round.