There is no 13th floor. It's part of a computer-simulated universe.
In 1999, Hannon Fuller and Douglas Hall create an astoundingly exact computer simulation of Los Angeles, circa 1937. Better yet: a user can exchange minds with a simulated character by downloading himself into it. The downloading, or "jacking," has not yet been safety tested but, unknown to the team, Fuller has already been secretly downloading himself into the system to live the high life of wealth, booze and screwing 1930s showgirls.
Somehow, Fuller discovers something very important about "limits of the simulation" and leaves word of it in 1937 with a bartender named Ashton. Fuller tells Ashton to give the letter to Hall when he comes for it. Upon returning to 1999, Fuller has just called Hall to tell him about the letter when he is brutally stabbed to death by an unseen assailant. Hall - with no memory of the incident but finding a bloody shirt in his laundry - becomes the prime suspect in Fuller's murder and begins doubting his sanity. To find the letter and to discover who killed Fuller, Hall must jack into the system.
Unfortunately, Ashton read the letter and from it assumes that Fuller meant his world (1937) is a simulation. Ashton loses his mind. What Ashton doesn't realize, and what Hall eventually learns, is that Fuller wasn't talking about 1937. Fuller had discovered that THEIR world of 1999 is a simulation, too.
Jane, the mystery girl posing as Fuller's daughter, has fallen in love with Hall and tells him the truth: She is from a higher reality (the year 2024) and Hall's world IS a simulation - the first simulation ever to create another simulation within itself. She and her husband David jack into thousands of simulated worlds. Problem is, David has become insane with power and murders simulated people for fun (in his mind, they don't really exist). It was David, jacked into Hall, who murdered Fuller, presumably for his discovery of the 1999 simulation.
David suddenly jacks into Hall again and attempts to kill Jane for her betrayal, but is himself killed by a cop who has somehow figured it all out. David, in Hall's body, dies in 1999. Hall wakes up in 2024 (since his body "died" it took David's "soul" with it, Hall now inhabits David's body in the "real world"). Hall and Jane begin their new, shiny life together...but just before the credits the screen flicks off like a monitor, implying that the 2024 world may itself be a simulation monitored by an even higher reality.
Thanks Robert W (Pooper), and Moore (Long Version)!