Cerberus is a human supremacist paramilitary organization in the Mass Effect series. While declaring themselves as being dedicated to the advancement of humanity, both the Citadel Council and the Systems Alliance designate it as a terrorist organization. The organization served as minor antagonists in Mass Effect, an ally in Mass Effect 2 and major antagonists in Mass Effect 3. Overall, the entire group serves as the secondary antagonists of the series. The organization is headed by the Illusive Man.
According to Admiral Kahoku, Cerberus started out as a Systems Alliance Black Ops group, having complete access to Alliance activities. However, the group went rogue and broke away from the Alliance, conducting many unethical experiments. In reality, Cerberus was founded by Jack Harper, a human mereanary who fought in the First Contact War. During this time, he and his partners, Ben Hislop and Eva Core, discovered a conspiracy led by turian general Desolas Arterius to transform the turians into supersoldiers using an ancient alien artifact. While they managed to thwart the general's plan with the help of his brother Saren, Hislop and Core lost their lives in the process. This made Harper realise that while possessing knowledge and wealth, the galaxy was a dangerous place and humanity was about to enter dark times. As such, he released a manifesto calling for an army, a 'Cerberus', to protect humanity from any threat beyond the Charon Relay, declaring that an alien attempt at human genocide was an inevitability. The manifesto was denounced as 'survivalist rhetoric written by an illusive man', and eventually fell off the media radar.
However, in 2165, terrorists stole antimatter from the SSV Geneva; the sole figure arrested named his sponsor 'Cerberus'. From there, the organization continued to expand, gaining funding via a series of front companies and agencies, while also experiencing and increase in recruitment and conducting savage experiments on human and alian subjects.
In Mass Effect, Shepard can disrupt Cerberus operations and may discover the organization may be indirectly (and in some cases directly) involved in some side missions. Apart from this, the organization serves no purpose in the main story.
In Mass Effect 2, Cerberus uses its resources to fund the Lazarus Project to bring Commander Shepard back to life after he/she was killed by the Collectors. The project was headed by Miranda Lawson, Cerberus' top operative. Once Shepard was revived, the Illusive Man explains that the reason Cerberus brought him/her back to life was that human colonies have been disappearing. The Citadel Council refuses to investigate but Cerberus is the only organization willing to take action. During the game Shepard can discover more unethical experiments done by Cerberus, such as their research on Pragia (though they claim this was a cell that had "gone rogue") and Project Overlord.
In Mass Effect 3, Cerberus attempts to find a way to control the Reapers, in order to make humanity the dominant species in the galaxy. The organization has gone as far to use Reaper technology to indoctrinate war refugees and create soldiers loyal to the Illusive Man. Shepard first encounter Cerberus on Mars, looking for data on a Prothean superweapon. Commander Shepard is able to stop them and acquire the data on the weapon, which the Alliance begins constructing in order to destroy the Reapers. Throughout the game, Cerberus attempts to undermine Alliance operations and Commander Shepard's mission to the unite the Galaxy against the Reapers. Eventually, an attack is launched on the Cerberus Headquarters by the Alliance, effectively ending the organization. Later, the Illusive Man dies onboard the Citadel, putting a definite end to Cerberus.