5-10-16 UPDATE: Here is one way it could be done …
Runners on 1st and 2nd or bases loaded. Less than two outs. Infield pop up. Infield fly is declared and the batter is out. Out #1. The runner on 1st base thinks there is two outs and takes off on the hit and passes the runner at second base and is called out. Out #2. The runner steps off 2nd base and is hit by the ball coming down. Out #3.
Thanks to those who answered correctly!