The Nature of Cerberus

Exhibit A:  Cerberus is a human supremacist organization dedicated to the domination of humanity throughout the Galaxy with no regard for the Civil Liberties of others - We see this most clearly in their occupation of Omega, the only time that we have seen Cerberus in control and ruling an area, with them controlling the population and setting up specific quarters for them seperating them one from another.  And with them disarming any of the population of Omega who was not human.  

However at the end of ME 1 which transitions into ME 2 Shepard is left with a choice and a cosequence revolving around what happens to the Council and the resultant state of the galaxy in ME 2.  

For a Renegade Shepard which killed the Council the Alliance decides to establish a human only Council which sets up extreme curtailing of the Civil Liberties of the cultures throughout Council Space and proves to be extremly unpopular with the other species resulting in some pretty bad relations.  This government is, essentially, a mirrored outcome of what Cerberus wants to achieve.  

For a Paragon Shepard which kills the Council the Alliance sets up a Council with a human chairman...which then proceeds to curtail civil liberties and is unpopular with their alien allies though maybe not as much so.  

For a Shepard that preserves the Council, while this is an option which preserves the most liberty and while I have not done this in a while so the details are foggy in my mind...I do believe they still esstablish travel restrictions and restrictive security checks for 'geth infiltrators'...which again the funny part is such meassures are stupid when dealing with the geth in the first place and is really amounts to the Council/Alliance cracking down just because they can.  

So in either case the Council/ Alliance decides to take more control over their political sphere of influence and the Alliance especially, if they get the chance, tries to take over as the dominant force of the Galaxy, no different then what Cerberus is trying to do.  

Also keep in mind while a bit more understandable considering this is what I would do if I were them, it is hardly against the so called attitudes the Council and the Asari typically hold...but in ME 3 we discover that the Asari has used a Prothean Beacon on Thessia to take political and economic control of the galaxy.  They do not share this technology and has used it to establish Asari dominance throughout their sphere of influence...exactly like Cerberus plans to do with the Crucible/ Reapers.  

Exhibit B:  Cerberus, as terrorist organizations do, use violence and cohersion to achieve their ends, mass murder, political assassination, etc.    Admiral Kahoka and I do believe they were tied to a few other mass casualty events...and even before the events of ME 3.  

But the Council has a branch specifically devoted to black ops, specifically designed to use these sorts of tactics, and specifically tasked with being above the law.  The Spectres.  It is quite telling to me that out of the four Spectres we meet in the trilogy only one of them is a legitimate through and through good guy.  Saren Arterius was a *rogue Spectre* who engaged in several morally questionable activities, the attack on Eden Prime, Anderson's story, and his own apparent racism against humanity.  Tela Vasir who leases her activities to the Shadow Broker and engages in terrorism on his behalf...the bombing on the Drakon Trade Center.  And then Commander Shepard herself, which can be played as being quite the ruthless ends justifies the means mustache twirling racist throughout all of ME 1 and ME 2.  Hell in this vein too the Council has no problem with Shepard working for Cerberus and giving her her Spectre status back in ME 2.  My Shepard usually tells them to shove it but it is telling that the Council has no issue with Shepard working with Cerberus, a terrorist organization, an avowed enemy of the Council, etc, as long as they could enforce their will.  And on top of this the Council has the rather nasty habit of looking the other way when their agents commit mass murder as long as a reasonable scape goat is made be it Cerberus, the Geth, Anderson when Saren Arterius blew up the refinery, or Cerberus and Shepard when Tela Vasir blew up the trade center...given their history she is probably right that the Council would just blame Cerberus instead of launching an investigation.  

And before anyone says this is just the crimes of the modern organization one of the first logs in the Citadel Archives is them recruiting the first Spectre, a Salarian.  He is cold, aloof, semeingly psychopathic, I am quite sure a criminal at the time, and they let him know they are recruiting him specifically for his more aggressive tendencies.  

Exhibit C:  Cerberus engages in medical experiments on their fellow humans and other sentient life forms.  Admittedly this is Cerberus at their worse and given the scale and repeated uses of this this is still much worse then the Council themselves but it is still worth nothing there is a big three hundred pound gorilla in the room.  

The Genophage.  Approved, developped, and then utilized by Council Governments against another species.  Now this might be a bit of a stretch but I would think that its development would involve live Krogan test subjects, just like Cerberus with David Archer, and its utilization meant the Council was just fine deploying a bio weapon against the Krogan which fundamentally altered their genetics and ended up causing countless, literally countless, numbers of still born deaths and this is to say nothing of the socialogical consequences.  So much so that many Krogan in the universe claim that this is basically long game genocide and that is certainly a reasonable assessment.  

And this attitude continues well into the modern era resulting in a genophage modification project being approved by the Salarian Union and Dalatrass Linron being quite insistent it was still the right thing to do all the way up till the Reaper war in 2186.  

Now like in a lot of ME situations there is a lot of justification for the initial deployment of the Genophage given it may have been the only choice between that and A. Living under a Krogan Empire or B. the end of all life that is not Krogan/ their own genocide/ Krogan being genocided right then and there.  So...yeah.  But the issue is as comparatively good as it might have been it was still a pretty evil action which Cerberus has also done...well honestly a lot less now that I am thinking about it.