Cerberus is an independent and outlawed paramilitary organization focusing on human dominance in the galaxy via technological, military and biotic supremacy. At the helm of Cerberus is The Illusive Man who directs Cerberus' operations although the organization is structured in isolated operational cells so that no one cell knows all of the operational details of another. The Illusive Man's true name and history has either been lost or redacted and few details are known about him excepting that he first arose shortly after the Battle of Shanxi (2157, also known as the penultimate battle in the First Contact War).
Cerberus' operations are funded through various, legitimate front operations such as Cord-Hislop Aerospace, a Terran shipbuilding firm. Cerberus pursues its objectives through a variety of different activities including, but not limited to: human experimentation, support of legitimate political parties such as the Terra Firma party, advanced shipbuilding, artificial intelligence and study of exobiology.
Cerberus hires former Alliance personnel, mercenaries, assassins and bio-technicians. They are extremely violent and partake in illegal and unethical experimentation on human and alien life forms, including the remaining Rachni and husks. During the course of the first Mass Effect, Commander Shepard encounters several Cerberus labs as side missions. Upon discovery, Cerberus members always become hostile and a firefight breaks out.
Mass Effect: Ascension
After the events of Mass Effect, Cerberus focused its interests on biotic research, viewing an advanced human biotic as being the only thing that can save humanity from the oncoming attack of the Reapers. In Mass Effect: Ascension, by Drew Karpyshyn, many human children are kidnapped and experimented on in an attempt to isolate biotic abilities and increase their strength in a manner similar to what Kaiden Alenko went through.
Cerberus has also taken a great interest in the quarians, believing they have the secrets that can help defeat the Geth and eventually get an upper hand against the Reapers.
Mass Effect 2
Despite Shepard's destruction of its installations and interference in its plans, The Illusive Man directs his Cerberus operatives to go to great lengths and expense to acquire Shepard's corpse, reanimate him and prepare him for his role as humanity's savior. In the process, Cerberus builds the Normandy SR-2, a stealth frigate similar in design to, but almost twice the size of its predecessor, the SSV Normandy SR-1.
The Illusive Man and Cerberus observe Shepard and the crew closely as both are aware that their alliance will only last as long as their aims coincide. The Illusive Man never issues commands to Shepard but is not above withholding information from Shepard or putting him in positions in which he has no choice but to carry out missions beneficial to Cerberus but not necessarily to the Alliance or Citadel Council. During this chapter of the Mass Effect Saga it becomes clear that Cerberus as an organization pursuing human dominance over other species is not equivalent to the individuals who make it up as exemplified by Yeoman Kelly Chambers, Miranda Lawson and Jacob Taylor. It also seems that The Illusive Man and, by extension, Cerberus is more interested in the ends than the means and is not opposed to working with alien species so long as the relationship furthers its pursuit of human dominance.
In the climax of ME2, Shepard can choose to hand over a facility of great value over to Cerberus or to destroy it, angering The Illusive Man. It is also possible for a Cerberus-defiant Shepard to see Miranda Lawson resign her commission during these events.
Mass Effect: Retribution
The events in the 3rd Mass Effect novel take place after Mass Effect 2. The Illusive Man is intent on studying the effects of Reaper technology on Humans. He has a former Cerberus agent by the name of Paul Grayson implanted with Reaper tech, similar to the technology implanted in the rogue SPECTER Saren Arterius in Mass Effect. The experiment is allowed to progress unchecked in order to study the effects and attempt to find a counter for the changes, whether through reversing the effects or finding a combat-related weakness.
Grayson manages to get a mysterious message to Kahlee Sanders before his abduction which prompts her to approach Captain David Anderson for help (for the purpose of the expanded-universe novels, Ambassador Donnel Udina rather than David Anderson was chosen to represent humanity on the Citadel Council). They know they cannot fight Cerberus alone nor turn to the Alliance due to Cerberus' infiltration of the upper ranks of its officer corps, so they turn to the Turians. With some help from the Turian military, they strike back at Cerberus causing the now infected Grayson to escape into the galaxy, now under Reaper control.
The chase for Grayson leads Anderson and Kahlee across the galaxy and into the clutches of Aria, the Queen of Omega, and back to the Ascension Project biotic school where Kahlee used to work. The effect of the Turian assault and Grayson's subsequent attacks and escape leave Cerberus crippled and the Illusive Man struggling to rebuilt his once vast empire.
Mass Effect 3
Cerberus returns in Mass Effect 3, this time being a main enemy for the rest of the game.