All went well until late September, when, in a St. Louis bar—another straight bar—Pallone met two brothers, one of whom "kept hitting on [him] all night." At the end of the evening, the brothers begged a ride home and invited Pallone in, but then abruptly told him to leave. Immediately thereafter, the new story of a pick-up in a bar was swirling through baseball. Pallone surmised that someone may have orchestrated the set-up.

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That fall Pallone worked the play-offs on a crew that included Engel. At dinner after the first game, Engel asked about the new rumor. Pallone could no longer bear dissembling, and so he came out to Engel and his wife, Pat, who had also become a good friend. Both Engels received the news with equanimity: Pat Engel said that she already knew (thanks to "woman's intuition"), and Bob Engel "suspected" Pallone's sexual orientation. Both pledged and gave their continued friendship.

In April 1988 Pallone was in the middle of one of baseball's most famous mêlées. In a game between Cincinnati and New York, with the score tied and two out in the top of the ninth inning, Pallone called a Mets hitter safe at first base. Instead of attending to the action of the game, the Reds' first baseman argued the call, allowing a New York runner to score what proved to be the winning run.

Volatile Reds manager Pete Rose raced from the dug-out and began berating Pallone for having taken too long to make the call. In the course of the confrontation, Rose shoved Pallone—grounds for immediate ejection—and then did it again. The other umpires arrived to restrain Rose and remove him from the field.

Meanwhile, the Cincinnati broadcasters had been denigrating Pallone. The crowd, listening to their radios, responded by throwing whatever they could—including a boom-box—at the umpires, who had to leave the field for their own safety.

After the game, Rose claimed that Pallone had poked him in the face during the argument. Game film put the lie to this, but incensed fans called Pallone's hotel and made death threats.

Giamatti imposed a thirty-day suspension and a ten-thousand-dollar fine on Rose and reprimanded the broadcasters for their role in inciting the dangerous behavior of the crowd.

Pallone regarded Giamatti as something of a father figure who had his best interests at heart. In a conversation about a month after the incident in Cincinnati, Pallone came out to him, and Giamatti told him that his sexual orientation made no difference to him "as long as it doesn't interfere with the game itself."

In September 1988, however, Giamatti, newly elected to the post of Commissioner of baseball, called Pallone to his office and offered him the choice of requesting a leave of absence or being forced to take one because the district attorney of Saratoga Springs, New York was about to investigate him in connection with a ring of men having sex with teenage boys. Pallone knew and had visited two of the men and was aware of the scandal, but he assured Giamatti that he was not involved. Giamatti refused to budge, and Pallone requested leave.

A few days later a newspaper article falsely reported that Pallone had resigned. Stories about the district attorney's investigation quickly followed.

The district attorney's office had two accusers against Pallone, a fourteen-year-old boy and an anonymous adult who had appeared in television interviews with his face and voice disguised and who claimed to have identified Pallone from baseball cards. (Baseball cards of umpires do exist, and there was a 1988 Pallone card; nevertheless, finding one would have been relatively difficult.)

Pallone's two acquaintances, both already sentenced, exonerated him, and the anonymous adult accuser added to his previous criminal history by getting arrested twice more on unrelated charges and was dismissed as a credible witness. The motives of or pressures on the fourteen-year-old remain unknown, at least to the public.