The murder of a man named Ibundan (Stephen James Carver) who Odo had sent to prison several years earlier leads a number of Bajoran citizens to suspect Odo himself killed the man. Led by Zayra (Edward Laurence Albert) and their own prejudices, the suspicious Bajorans take on a personal mission against Odo.
A substantial step down from the pilot and "Past Prologue," there are some big problems with "A Man Alone." The "murder mystery" is a rather uninspired plot device to be using on only the second regular episode, and the investigation proceedings are not very adeptly written.
The idea of Odo being a suspect is handled reasonably at first (particularly in an unsettling display of Odo attitude when Sisko temporarily relieves him of duty), but the ultimate result of the Bajorans forming a mob outside his office and screaming shapeshifter epithets is a misguided and excessive approach to highlight the issue. It's staged poorly and feels forced. You'd think that considering Odo has been on board the station four years the Bajorans would be used to the idea of his presence. The technobabble-heavy solution that reveals Ibundan cloned himself so he could kill the clone and frame Odo for the murder is far-fetched at best.
As compensation for the murder plot, there are number of small, relevant character threads, including Keiko O'Brien feeling the burden of uselessness aboard a station she isn't happy living on, and her solution to create a school for the station. The Dax/Sisko/Bashir interaction is also somewhat refreshing. But the episode wanders too much.