The second season began airing in the United States and Canada on August 21, 2006. The story continues eight hours after the prison escape from Fox River State Penitentiary, focusing mainly on the escapees. New characters are introduced, including a federal agent Alexander Mahone (William Fichtner), who is assigned to track down and capture the eight escapees.[17] "The Company" continues their plan to locate and eliminate Lincoln Burrows and others who get in their way. Furthermore, the position of the characters remain ambiguous as more characters become involved in the conspiracy plot.

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