Naturally, if the villain gets killed the little boy dies. But unless the crook is caught again, his son might live but other innocents might not. The biggest plothole is the San Francisco hospital that sets most of this movie. Desperate Measures has some decent twists and turns, but everything has been done before. Eggheaded evil is old hat.
Evil geniuses are an action-movie perennial anyway.
Michael Keaton acts like he's Jack Nicholson doing Hannibal Lecter, and Garcia doesn't work as a Bruce Willis clone. This movie is one big obstacle course for the two leads to run through before the predictable finish.