The storyline of Blitz: The League II follows a rookie player, nicknamed "Franchise" who will be the first ever player to play both sides of the ball. He represents the player's created player and the creation process will take the form of a press conference introducing him to the media. The story will also once again involve taking a team from Division III to the League Championship of Division I. Due to the increased number of teams, the League schedule has been shortened, meaning that the story will now take place over three full seasons. Franchise also takes the place of the rookie from Blitz I.

The player's main rivals this time around are the Los Angeles Riot, a new team in The League specially built by its owner to win championships every year. The Riot's roster now includes Bruno Battaglia, who played for the player's team in the previous game. It is speculated that Battaglia will be the main individual antagonist for the game, much like Quentin Sands was during the first Blitz game. The reason for the rivalry has to do with the fact that the commissioner wants the Riot to be the new face of the League and does everything he can do to help them out including starting them in Division II and giving them the first pick in the draft. He expected Franchise to be taken with this pick but Franchise shocks everyone when he declares he'll only play for his hometown team, the Player-Created Team. This causes the rivalry between the two teams and puts Franchise and the player's team on the commissioner's bad side. Two games into the Division III season, Sands is traded to the player's team from the New York Nightmare. However, he is considered past his prime due to his age and knee injuries he suffered after the first game. However, Sands can be returned to his prime through proper training and drugs. Sands takes on the role of the veteran for the player's team, since he has been in the League longer than Franchise.

After winning the Division 3 championship, Franchise gets sent to jail after he tests positive for the drug Ultranol. This comes about as a result of Quentin Sands spiking his drink at a nightclub. The warden convinces Franchise to play for his prison team against a rival facility in their annual game in exchange for an early release. This game will consist of no pads and a 30-yard field and also feature an appearance by Mike Mexico. After the prison game, the player may add one of the team captains from Division III to his own team. Five of seven are offered, with two omitted at the positions Franchise plays, unless Franchise does not play the same positions as the other 7 team captains, in which case, all seven are offered as choices (this would come about if Franchise is a TE/LB or TE/CB as none of the seven team captains of Division III play those positions).

After a Division 2 win against the Los Angeles Riot, Bruno Battaglia and the Riot show up at a nightclub where Franchise and Sands are and it is revealed to Franchise that Sands spiked his drink. This sparks a brawl between the two players, and leads to animosity between them for nearly the remainder of the game.

After winning the Division 2 championship the Commissioner comes into the press conference and announces the Minnesota Reapers are not competing next season due to the drowning of seven players. He announces the Riot will be taking their place in Division 1. At this time, Karl Tirpitz (who, like Quentin Sands, is also a defensive player), captain of the Supermax Prison Facility team, signs with the player's team for the Division I season.

Right before the Division 1 Championship game Quentin Sands goes to the commissioner's office and tells him that Franchise has injured his achilles and will not play in the game. Acting on this information, the commissioner tells the people in his office to buy stock in the Los Angeles Riot. Sands waits outside the door and tapes this conversation. After the player's team wins the Championship against the Riot, the commissioner is arrested for insider trading, money laundering, and extortion.