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The Freaks that roam Pacific City in Crackdown 1 are -not- related to the Freaks that roam Pacific City at night during Crackdown 2. This is a common misconception.

Crackdown

During the events of Crackdown, you need to take out Dr. Baltazar Czernenko as a part of the Shai-Gen Corporation. Dr. Baltazar Czernenko used to work for The Agency as a researcher, creating the Super-Human and cloning programs. After he left The Agency and started to work for the powerful Shai-Gen Corporation, he did numerous test on Pacific City residents, trying to create stronger and overal better Super-Humans to work for the Shai-Gen Corporation. He never managed to create what he was looking for, but after the player takes out Dr. Baltazar Czernenko, located at the Institute of Research, all the cages where the Freaks where residing in open, and let all the Freaks get out of the facility. They soon take over the area around the facility, and are often engaged by The Agent, The Agency and the Shai-Gen Corporation. The Freaks cannot be erased from the city. This is to keep the player playing. After all the gangs are defeated there wouldn't be any resistance in Pacific City, and the game wouldn't be 'playable'. 
 

Crackdown 2

The Freaks -or abominations- in Crackdown 2 are the result of Catalina Thorne's plan to take revenge on The Agency and Pacific City for firing her after they found out she was conducting her own research. She was researching the M2448 Virus, used to create the Abominations that haunt Crackdown 2 during the night. These Freaks are engaged by The Cell, Thorne's own gang, and The Agency. Residents of Pacific City don't leave the specially created 'Safe Zones', where the Cell hold guard and the Freaks are shot on sight.

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