The story begins as an incomplete continuation of the previous chapter. It starts out with Gina attending Brian's funeral, and it is noted that she is the only mourner in sight.
The introduction shows the eye of a crow, fading out to show Brian's funeral, where there are only four people: a priest, who is speaking in Latin; Luane, who is the cemetery's manager; Ernie, who is the Happy Dale Mental Hospital security guard; and Gina, Brian's girlfriend. This scene is spliced with flashbacks to a trial, where Brian is accused of apparently killing General Kordsmier, but due to a case of amnesia, he is deemed insane and locked away in a mental institution.
Chapter 1: Brian Basco is Dead
After the funeral has ended, Gina receives a call from Brian, who tells her to save him, because he's trapped in his own grave. He ends the call because his battery is very low. Just before the battery dies, he sends a message to Gina.
Chapter 2: The Art of Running Away
Gabbo, a friend of Brian's from the asylum, tells Gina the story about how Brian escapes. Gabbo tells Brian a plan, but Kurgan steals the plan and runs off to use it himself. With a bit of improvisation, Brian overcomes these obstacles but stops part-way through the escape as he finds Kurgan decapitated.
Chapter 3: A Timely Suicide
In a cabin out in the woods, Gina helps a psychologist investigate the death of a witness that would have exonerated Brian. His death had been ruled a suicide.
Chapter 4: An Unexpected Ally
The story of Brian's escape resumes, as we learn how he plans on using Kurgan's body to look like his own.
Chapter 5: Deconstructing Brian
We finally learn some of what happened between the ending of Runaway 2 and the opening of this game. Also, Gina gets tied up as Tarantula catches up with her.
Chapter 6: The End is Here
Brian comes up with a plan to defeat Tarantula and her goons, exonerate himself and rescue Gina. The series is brought to a fitting ending.