The storyline of Crackdown isn't very intricate, it is very simple, beginning and finishing near the start of the game, and then the whole game is storyless. This is not a bad thing, because the story gives you good reason to want to finish the game.
When you start the game, a voice is telling you about "The Agency", saying that the Agency is mutating humans, using a formula produced by the Shai-Gen Corporation's Dr. Baltazar Chernenko. They mutate humans to make them more powerful, stronger, faster, smarter, and more immune to being hurt. After describing this, he tells how the world's police forces had all combined to create "the Agency", which is really a world-wide crime fighting orginazation, with the police now being called Peacekeepers. The voice tells you that the Agency made it's headquarters in the world's most crime-filled city, which also is the capital of the nation, Pacific City. He goes on to explain that the city is divided into three main islands, each controlled by a different gang. The East island is controlled by Los Muertos, a Central-American based drug-dealing gang, who do not command respect, but get it from the city's citizens by causing crimes to scare the people. The West island is controlled by the Volk, a Russian-based gang filled of illegal immigrants and immigrant workers from Russia. The East island is also the working district, fitting in with the type of gang members the Volk have. The North island is controlled by the Shai-Gen Corporation, a highly-organized, Japan-based gang, whose members are usually owners of a succesful business. The North island is the financial district, which fits in with the type of members the Shai-Gen have.
After explaining all this, the voice tells you that you are the Agency's newest super-human member, and that it is your job to clean the streets of all the gangsters from each of the three gangs. He tells you that to do this, you must locate and eliminate the kingpin of each of the three gangs. To be able to kill the kingpin more easily, he sais that you should take down his four generals and two lieutenants, harming the gang in six ways: halting communications, weapon trafficking, explosives trafficking, hitman training, member recruitement, and transportation. Every time you accomplish one of these things, the kingpin's defenses will be weakened, meaning that it will be easier for you to kill him. You are then thrown into the city, and it's then up to you to figure out how to clean the streets. There is no story in between now and the end of the game, save for the moments when you kill important members of the gang. When you do, the voice tells you how the gang is affected, because of that member's death. After killing the kingpin, the voice tells you how the island was trasformed and re-named, and how the citizens are living easier now.
After killing every single member of every single gang, the voice then says:"Congratulations Agent. Peace at last. You overthrew the world's most evil criminal masterminds and their dominant empires. You have returned law and order to Pacific City. You gave the people back their lives. Thank you." After a moment of chuckling, he says: "It's taken years of meticulous planning and patience to reach this stage. But it was worth it. Who do you think supplied Los Muertos? Who do you think turned a blind eye to the Volk's activities? Who do you think was Shai Gen's biggest supporter? Who do you think ran organized law enforcement, and ran it into the ground? The people had to experience absolute anarchy before they would accept unconditional control. You are the portent of a new world order, Agent. Pacific City... was only the beginning."
And so ends the game of Crackdown. If you want, you can go back to gang-play, with gangsters on the streets, so that you can rack up some achievement points for yourself. But otherwise, the game is now over. No more story, missions,crimes, nothing.