In Season 3, after Jim shot and killed a Turkish exchange student, Bayliss tried to shoehorn himself into his partner Frank Pembleton's investigation.

Meldrick Lewis that he was once arrested for protesting U.S. policy in El Salvador when he was a teenager, a story idea that Secor reportedly disdained as out of character for Bayliss.

In the Season 4 episode "Stakeout," he learns that Risley Tucker (Moses Gunn), an arabber who was the prime suspect, has died of natural causes.

Bayliss becomes obsessed with the idea that the two cases are connected, to the point that his actions begin to jeopardize Pembleton's efforts to get a confession.

In the Season 6 episode "Finnegan's Wake", Bayliss wrestles anew with the Watson case when he learns about the longest-running unsolved homicide on the BPD's books, the rape and murder in 1932 of a little girl named Clara Slone.

Yet Pembleton also saved Bayliss from being charged in an incident that could have been interpreted as robbery, and once told him that he was the only person he trusted other than his wife, Mary.

While Pembleton saw the world in strict black and white terms, Bayliss was far more open to accepting the shades of gray present in police work.

The case in the episode featuring his admission ("Betrayal") involved a mother who allowed her boyfriend to beat her daughter from a previous marriage and was pregnant with the new boyfriend's child; Pembleton showed some sympathy to the woman's story, while Bayliss repeatedly and forcefully berated the woman for her reluctance to stop the ultimately fatal abuse.

Pembleton left the force shortly after Bayliss was shot by a member of Georgia Rae Mahoney's gang in a gun battle.

In the first two seasons, Bayliss's character had been called a "fair-haired choir boy" and he stated once that he rejected the idea of having sex for any reason besides love.

The statement had something of a double meaning as it directly involved his unwillingness to argue with her about their problems, but other aspects of the character implied she also was referring to his disdain for rough sex.

At the end of the episode "Zen and the Art of Murder" it is implied he abandoned Buddhism as he feels having to shoot and kill a suspect who pulled a gun made him "not a very good Buddhist."

Bayliss' sexual orientation and religion had prompted him to develop a website, which was later shut down on request of Homicide Captain Roger Gaffney.

In the series finale he is outraged when Luke Ryland, "the Internet killer," escapes prosecution as the result of a legal snafu.

In Homicide: The Movie (2000), Bayliss was revealed to have taken an extended leave of absence, claiming that he had "things to think about" and issues (a point on which he is mocked by Meldrick Lewis).

The circumstances leading up to that result (Bayliss' arrest or death) are not revealed, but Pembleton later comments that he caught two killers that night.