James is a thirty-something software wiz with a drinking problem who runs away to San Francisco to escape a tragedy in his home state of Oklahoma. In front of his favorite pub one night, a teenage girl with a nasty bruise on her face asks for a cigarette. He sees her several more times and gives her food and smokes. She appears to be living on the street, running away from abuse. Late one night, the frantic teen, Amy, shows up at his China Town apartment. Having nowhere else to go, she seeks shelter and protection from her abuser, who could show up at any time. They form an unlikely and complicated friendship.

Bay City Runaway brings to vivid life the struggling, lonely alcoholic, the precocious, street-wise teenager, and the sexually-charged complication of a would-be girlfriend, Kyra, as their lives become intertwined.

It also captures 1990s college life as it tells the story of how a new friend, Zach, helps James win back the girl he will marry, leading up to the tightly kept secret of the tragedy that puts him on a plane to San Francisco in 2007.