Well, I did some major research, and I summarized everything that is available. Here you go, 
 
During the events of Crackdown 1, Catalina Thorne was working for the Agency. She worked there as a lab assistant. But files went missing and The Agency found out she conducted research of her own. They fired Catalina and she swore to take revenge at the Agency and Pacific City.  
 
This happens between Crackdown 1 and 2:  
The Agency didn't know was that she managed to create a virus, the M2448 Virus, that transforms people into freaks. A week after Catalina was fired she went into the lab and infected devices used on the Agents. They would go on a frenzy and then die. Resulting in the trashing of the Agency labs and the death of all Agents. They had to start the Super-Human and cloning program over. 
  
This happens just and during before Crackdown 2:
During this time Thorne infected people with the virus. Because they weren't genetically modified, they survived and turned into freaks. Because the Agency had a lack of Agents, the city got destroyed. Thorne used the hatred against the government to gain massive support. She recruited the revolting citizens and started a gang called The Cell. The revolting citizens are obviously unaware Catalina started the Freak epidemic. The Cell is up against The Agency and the freaks. They have "safe zones'' in which the residents of Pacific city seek shelter during the night. Because Thorne's success is depended on the the consistency of freaks, to scare the citizens, and their hatred against the Agency for the lack of support, Thorne has to carefully pick out what she does. For instance: She wants to destroy the devices against the freaks so she can keep the freaks around, and then tells the Cell and the residents that she the Agency means harm and they support the freaks. 
 
So the whole thing is based on the lie of a former research assistant who is responsible for all the trouble in the city in the first place.

YAY spoiler time!

Was any of that actually implemented in either game in any meaningful way?

" Was any of that actually implemented in either game in any meaningful way? "

I'm surprised that Crackdown's fiction is long enough to make a paragraph. Oh well I don't come to Crackdown for it's compelling story.

Wait what? Crackdown 2 has a plot? I never would have guessed.  
 
Seriously, the "plot" is about as deep as the story in Joe Danger. 

The first Crackdown was awesome, especially the little twist they had at the end.
 
Crackdown 2...not so much.

" @HandsomeDead said:

" Was any of that actually implemented in either game in any meaningful way? "

From what I heard. None what so ever. The main quest pretty much falls into" Kill the freaks little hidey holes" Rinse and repeat.  "

My post was written before the game was released
Was I close? For the people who have 'found' the plot of Crackdown 2...