Every Mass Effect player knows of the Genophage, the controversial sterility plague used against the Krogan species. The genophage appears in all three games of the original trilogy, though most prominently in Mass Effect 3 where the player has a chance to cure it (and an option to prevent it being cured). But even in the first two games it becomes a source of conflict. In the first game, tension mounts between Shepard and Krogan party member Urdnot Wrex when they find out Saren not only has a cure, but is using it to breed an army of Krogan slaves for the reapers. Depending on Shepard's decisions she can either convince Wrex to look at the bigger picture or watch as he dies trying to turn on her. The second game has a mission where the Shepard has to pursue a Salarian who is secretly researching a cure for the genophage, the outcome of which can have long-term consequences in the third game's Tuchanka missions.
There are many different views on the ethics of the genophage. Some see it as unethical and needlessly cruel, others say it was a necessary evil, and yet others argue it was entirely justified. Shepard gets to hear several different views over the course of the games, and even sometimes gets to express her own opinions. It is a multi-faced issue with no clear right or wrong answer. But regardless of which stance she takes its impact on the galaxy is constantly felt. The genophage may have been implemented before Shepard was even born, but she still witnesses the consequences of one of the most controversial actions taken by the Alliance.
Krogan Reproduction
Krogan evolved on the extremely harsh world of Tachunka. Even before its ecosystems were annihilated by the advent of nuclear weapons, it was a complex and dangerous ecosystem full of potential dangers. Much like how life evolved on Earth, life on Tuchanka had to adapt to innumerable challenges in an endless contest of survival of the fittest- species that were better at passing on their genes were more likely to survive. One evolutionary adaptation that early Krogan developed was one also commonly used on Earth- the ability to quickly produce large numbers of offspring.
At the time, this was a huge evolutionary advantage for the simple reason that more children increased the chances of at least some reaching adulthood and passing on their genes. However, as the Krogan became more advanced and eliminated many of the existing threats, mass reproduction tended to cause overpopulation rather than maintain a stable one.
Background: The Krogan Rebellions
The Krogan first entered the galactic community when they were recruited as soldiers during the Rachni Wars, and proved extremely effective. When the war ended, they were rewarded with access to planets previously owned by the Rachni. Unfortunately, the new colonies quickly became overpopulated necessitating expansion. As the Krogan population increased they had to keep building new colonies, but there was a problem- a lot of planets were already claimed by and legally belonged to other races.
This started the rebellions, which saw a campaign to conquer other worlds and drive out other races who were already there. Obviously, the council was not happy about this, and fought back with help from the newly-acquired Turian military. The Krogan were defeated, but their ability to quickly explode their population was an obvious threat. This is where the genophage comes in- acting as a way to keep the population from exploding to dangerous levels without resorting to complete extermination.
Impact on the Krogan
The majority of Krogan viewed the genophage as a slap in the face from the alliance and quickly developed a bitter resentment towards the Turian and Salarian races for their role in its creation. While it did succeed in its goal of preventing overpopulation, this was largely inconsequential to the various clans of Tuchanka that were more interested in competing for their own dominance. Most Krogan are eager to jump at the slightest chance of a cure, sometimes even when there are much bigger problems. This becomes a source of conflict with Wrex in Mass Effect, and heated political tension in Mass Effect 3.
The shame of living through the genophage also helped fuel a lot of the Krogan's violent urges. Even if they were fighting more often with each other, there was a common desire to seek revenge as soon as they were able. Depending on Shepard's actions, curing the genophage can actually start a second Krogan rebellion.
Additionally, the genophage had the unintended effect of shaping Krogan society. Because fertile female Krogan were harder to find, they were seen as an extremely valuable resource- one worth fighting and killing over. This created a heavily patriarchal society in which clans around Tachunka were locked in an endless war for access to fertile females- the ability to reproduce being a sign of strength.
Arguments In Its Favor
As unethical as the genophage may seem, and as it is often viewed, there actually are some good reasons for its implementation. The Krogan were known for two things- violent impulses and very fast reproduction, both of which consistently caused problems. Not only did the Krogan have an innate ability to cause violence wherever they went, but they also tended to overpopulate their homeworld. The Genophage offered a solution.
Limiting the number of fertile females put a cap on how much Krogan could reproduce. The idea was that Krogan would only give birth as much as needed for their species to survive. Some Salarians like Mordin Solus actually saw it as a means of protecting the Krogan for this very reason. It was also designed as a means of keeping the Krogan's warmongering tendencies in check. One of the Krogan's big advantages during the rebellion was ridiculously large numbers. Fewer Krogan makes them less likely to challenge other races.