Hmm...would this mean Reshiram would be associated with Black City and Zekrom with White Forest? Huh. Time to speculate! Let's see...
Black Version: The evil team goes after Zekrom in Black City. They succeed in capturing it. Sensing its opposite is in danger, Reshiram leaves White Forest and heads to Black City, searching for Zekrom. This throws out the yin-yang balance and your goal is to defeat Reshiram, stopping its panic/rage. You (with the help of Reshiram) then defeat the evil team and free Zekrom. After that, you earn Reshiram's respect, you battle again and you can catch it this time.
White Version: The evil team goes after Reshiram in White Forest. They succeed in capturing it. Sensing its opposite is in danger, Zekrom leaves Black City and heads to White Forest, searching for Reshiram. This throws out the yin-yang balance and your goal is to defeat Zekrom, stopping its panic/rage. You (with the help of Zekrom) then defeat the evil team and free Reshiram. After that, you earn Zekrom's respect, you battle again and you can catch it this time.