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Since the storyline of Street Fighter EX is an alternate storyline, it takes place around the time that the event depicted in Street Fighter Alpha would have occurred. As such, M. Bison is very much at large, and in the process of building up his Shadowloo army.
Guile awaits any news about his commander Charlie, who was last sent on a recon mission to discover the whereabouts of M. Bison's secret Shadowloo hideout. When no word is heard from Charlie in over a month, Guile begins to plead for the chance to lead a rescue mission, but his superiors refuse.
Then word reaches Guile about an underground Street Fighting tournament being held, reportedly hosted by M. Bison himself. Guile sees this as the opportunity that he's been looking for, and arranges to enter the tournament as a way to investigate the whereabouts of his commander and best friend.
During the tournament, Guile meets the interpol agent Chun-Li. At first, he is shocked to meet a woman who is such a competent fighter. Then he learns that she is a member of interpol, and that she is seeking revenge on M. Bison for the death of her father. He sees Chun-Li as a powerful potential ally, and conducts his investigation in cooperation with hers. Seeing the third EX tournament as a chance to take down M. Bison for good, he asks Chun-Li to be his partner, and she accepts.