Bases Loaded II continued the provision of a season mode, called the "Pennant Race" mode, which allowed players to keep track of statistics and scores over the length of a season. The fictitious teams remained from the original game, with the addition of a number of new players. A new addition to the game was the concept of biorhythm, which encouraged players to keep track of the biorhythm of each player on their team, in order to achieve optimal performance during the season. As well, the starting lineup and batting order was user controlled, and the view of the batter was changed from the first game.

Bases Loaded II continued the provision of a season mode, called the "Pennant Race" mode, which allowed players to keep track of statistics and scores over the length of a season. The fictitious teams remained from the original game, with the addition of a number of new players. A new addition to the game was the concept of biorhythm, which encouraged players to keep track of the biorhythm of each player on their team, in order to achieve optimal performance during the season. As well, the starting lineup and batting order was user controlled, and the view of the batter was changed from the first game.