The genophage bioweapon was created to end the Krogan Rebellions. From the start, the krogan had overwhelmed the Council. Only timely first contact with the turians saved the Council races. The turians fought the krogans to a standstill, but the sheer weight of krogan numbers indicated the war could not be won through conventional means. The turians collaborated with the salarians to genetically engineer a counter to the rapid breeding of the krogan.
The genophage virus gained the energy to replicate by "eating" key genetic sequences. Every cell in every krogan had to be altered for the weapon to be foolproof; otherwise the krogan could have used gene therapy to fix the affected tissues. Once a genophage strain could find no more genes to eat, it would starve and die, limited spin-off mutation and contamination. This "created" genetic flaw is hereditary.
The salarians believed the genophage would be used as a deterrent, a position the turians viewed as naive. Once the project was complete, the turians mass produced and deployed it. The krogan homeworld, their colonies, and all occupied worlds were infected.
The resulting mutation made only one in a thousand krogan pregnancies carry to term. It did not reduce fertility, but offspring viability. The rare females able to carry children to term became prizes the krogan warlords fought brutal battles over.
The krogan are a shadow of their former glory. While the Rebellions took place centuries ago, they are constantly reminded of the horror of the genophage and of their inability to counter it. The release of the genophage is still controversial, bitterly debated in many circles.