On July 15, 1998, while protecting an 8–7 lead over the Arizona Diamondbacks, Wagner was struck by a batted ball on the left side of his head behind his ear. Wagner was alert and conscious on the ground, and his vital signs remained good. He was carried off the baseball diamond on a stretcher, and it was found that he had suffered a concussion. He spent the night in the hospital. On the next day, he flew home to Houston, and he was also immediately placed on baseball's 15-day disabled list. Wagner worked on his balance and coordination for weeks before he was cleared by the team physicians to embark on a rehabilitation assignment with a minor-league team. After pitching there in three games, Wagner was recalled to the Astros on August 6, and he completed the rest of the baseball season there without incident. The Astros won a franchise-best 102 games while winning the National League Central division title and leading the league in runs scored. Their season ended with a defeat at the hands of the San Diego Padres in the National League Division Series.