After two years with Inter, Baggio decided not to renew his expiring contract due to his conflicts with Marcello Lippi, making him a free agent at age 33. He was linked with smaller Serie A clubs such as Napoli and Reggina, and also several Premier League and La Liga clubs, including Barcelona. Baggio ultimately transferred to Serie A newcomers Brescia, under head coach Carlo Mazzone, aiming to save them from relegation, and staying in Italy in order to have a greater opportunity of being called up for the 2002 World Cup. He was made captain and was given the number 10 shirt, playing as an attacking midfielder. Despite injury problems during the first half of the season, Baggio re-found his form and managed ten goals and ten assists in the 2000–01 season. Brescia finished in a joint seventh place, their best Serie A finish since the league’s re-establishment in 1946, and qualified for the UEFA Intertoto Cup, also reaching the quarter-finals of the Coppa Italia, losing to eventual winners Fiorentina. Baggio helped Brescia to the final of the 2001 UEFA Intertoto Cup, where they were defeated by Paris Saint-Germain on away goals. Baggio scored one goal in the tournament, in the final from a penalty. His performances earned him a nomination for the 2001 Ballon d’Or, and he finished 25th overall in the rankings. Baggio was one of the best offensive playmakers in the league, winning the Guerin d’oro Award in 2001, awarded by the Italian sports magazine il Guerin Sportivo, to the player with the highest average rating throughout the season with at least 19 appearances. At the start of 2001–02 season, Baggio scored eight goals in the first nine matches, leading him to the top of the Serie A goalscoring table. In his eighth league appearance of the season, against Piacenza, Baggio scored a goal but later suffered an injury. A week later, against Venezia, he scored from a penalty, but he endured a more serious injury following a hard challenge which caused him to tear the ACL of his left knee, keeping him out of action for four months. He suffered a second serious injury that season, tearing the meniscus in his left knee, after returning to the team, and coming off the bench, in the Coppa Italia semi-final against Parma on 31 January 2002. He was operated on 4 February 2002 and he returned for three matches before the end of the season, making a recovery in 76 days. On 21 April 2002, in the first game after his comeback, Baggio came on as a substitute to score two goals against Fiorentina, helping Brescia win the match. He scored again against Bologna, saving Brescia from relegation on the final matchday, and bringing his seasonal tally to 11 goals in 12 Serie A matches. Despite Baggio’s performances and public demand, Italy national team head coach Giovanni Trapattoni did not deem him fully fit, prompting the coach to leave Baggio out of the final squad for the 2002 World Cup. Trapattoni also expressed concern about bringing Baggio to the World Cup due to the presence of Francesco Totti and Alessandro Del Piero in his role, believing that this could create a rivalry between the players. After missing out on the tournament, Baggio reversed his initial decision to retire after the World Cup, expressing his intention to surpass the 200 Serie A goal mark.