About Cerberus army across the game

According to ME1, Cerberus is an Alliance black ops organization that recently went rogue. They are known for using humans for experiments, including thresher maw attacks, injecting people with thresher maw venom, creating husks with dragon's teeth they found, experimenting with thorian creepers and experimenting with rachni. They also kill Admiral Kahoku.

In ME2, they're a "pro-human" group and (based on other media) were actually founded much earlier than 2183 (time of ME1). Miranda always implies that those actions Shepard witnessed were roguish behavior, but the evidence doesn't support her. She turns a blind eye to Jack's situation, as well as to Cerberus invading the Migrant Fleet, and then there's Project Overlord. We learn later (in ME3), the TIM made sure Shepard only saw the parts the weren't so terrible but Cerberus lacks ethics.

In ME3, we see Cerberus until an indoctrinated TIM. The husks he had started to create in ME1 were now more refined to create foot soldiers. That's how Cerberus had so many of them. If you indoctrinate through partial huskification, then you've got loyal soldiers. We also learn that Henry Lawson figured out how to use the Reaper signal to the husks to control these people. Not all members of Cerberus are partial husks but they are all indoctrinated. The ones not indoctrinated are those we end up having to rescue and recruit. However, even Kai Leng was indoctrinated. The Prothean VI Vendetta says it detects indoctrinated presence just before Kai Leng walks up. He's clearly not a husk. I believe phantoms were created along similar lines as Kai Leng so are probably also not husks.

I agree. I was just trying to stick to what is presented to answer the question as best I could. However, I imagine Kai Leng was rebuilt with current Cerberus tech. That stuff all had to be Reaper tech. Kai Leng might not be indoctrinated on the level of the Cerberus troopers but probably was in the same way as TIM. Low level, still highly functional and independent, but in the service of the Reapers. I just can't imagine anyone not indoctrinated would take on Shepard, attack the Citadel, etc.

I always headcanon that Benning were Cerberus troopers that TIM lost control of and fell under the sway of the Reapers. But, yes, it's weird that they never followed up on it.

But Hackett goes on to say he believes Cerberus. Why plant that in a player's head if you're not going to follow it up? Players expect a resolution when stuff like this is brought up.
Just as niggle though.

I thought that remark by Hackett was really weird, too. Especially in one playthrough, when I recruited Javik just before heading to Benning. On Eden Prime, Shepard and company walk into a room full of blood and corpses with a big screen and a few beer bottles lying around. Their comments:
Shepard: "Shot in the back while watching the game."
Squad mate: "This was someone's home."
(or something to that effect)

Yea, not shooting civilians my ass. And as you say, there was never any follow-up to that notion that it might be a rogue cell on Benning. I wonder if there was some cut content in relation to that one...

Anyway, here is to Bilal. He never hesitated. Without him, none of us would be alive.