During the " Duck Knight returns" arc, It was unknown who was behind the company. However, it turned out it was Darkwing Duck's very first enemy: Taurus Bulba.
Following Bulba's defeat, Scrooge took it over and gave the CEO title to Launchpad.
Taurus Bulba revealed that the Quackwerks Logo is actually Darkwing's profile.
Bulba also revealed that he created the cooperation to control St. Canard and also to use its citizens to unlock the Gizmo Duck armor for his own selfish purposes.
Crisis on Infinite Darkwings
Launchpad used the Quackwerks Crimebots to defeat the Darkwings of the Multiverse.
It is revealed that when Quackwerks was taking over St. Canard, it also got members of both F.O.W.L. and S.H.U.S.H. to join its ranks as employees just like Darkwing did. In order to outdo Quackwerks, the F.O.W.L. High Comand began to figure out a way to summon a being who could control not only St. Canard but also the world it self: Duckthulhu!
When Magica De Spell and the Phantom Blot were taking over the city with their evil-making ink, they took over Quackwerks.