Having played it a little more, I suddenly realise how little story or character development Crackdown (either game) has. I never really thought about it like that in the first game, but it's true. Crackdown has all the plot and character development of an old Mario game. Which is surprising for a modern action/shooter/sandbox title.
The story is that mutant freaks are roaming the city for some reason, and a group called Cell is fighting the Agency. The Agency want to use something called Sunburst to destroy the freaks, and to do that they need to activate a lot of charge units, which are under Cell's control. Once one circuit of units is active, a beacon appears, and you have to protect it from freaks while it charges.
Now, while that sounds like at least a somewhat decent amount of plot, it is all explained within about 10 minutes. After that, it's pure gameplay as you just go to each location, defeat enemies, and activate beacons. There is literally one mission in this game, which is go somewhere and kill everyone. Like I said, it's basically the sandbox/shooter equivalent of Mario.
You also have to establish Agency drop points, so you can order in weapons and vehicles and stuff, by taking over Cell strongholds. But it's the same mission of getting to the location and killing everyone there. It's actually a lot harder than the main mission of charging the beacons too, because the charge units aren't heavily guarded at all. There's freak breaches to stop too, which is the freak equivalent of Cell strongholds.
There's some gameplay flux between day and night, which is the only real change from Crackdown 1. Freaks, and freak breaches only appear at night, and because of this Cell retreats from the streets at night. So Cell strongholds will be tougher to take on at night.
Other than that, there's is really no difference between the two games, other than the usual new weapons and such. It looks exactly the same as the first, with slightly worse character design/models for the Agents to my eyes. It's the same city as well, and the map hasn't been changed at all from what I can tell, other than surface changes to make it look more rundown.