The Single Player mode of MM8BDM is essentially a play through all the maps in the game with set bots. After so many levels, the player fights special bosses exclusive to singleplayer.
The story of the game takes place one year after the events of Mega Man 6.
After Mega Man defeated Dr. Wily for the 6th time, the real Mr. X was found and rescued. In celebration of his heroic efforts, Mr. X hosted the second annual robot master tournament with new rules and arenas. With permission from Dr. Light, each robot would have to be reprogrammed use the weapon swapping abilities of Mega Man to keep the competition fair.
During the final announcement of the tournament, Mega Man and Dr. Light's television is interrupted by Dr. Wily. He states that the tournament is a great idea, and that he wishes to prove his genius by entering all his robots to prove once and for all that Dr. Wily is superior to Dr. Light. With no leads on where Dr. Wily could be hiding, or what he could be plotting, Dr. Light decides to enter Mega Man and his other creations to the tournament to ensure Dr. Wily doesn't have anything hidden up his sleeves...
The player starts in Dr. Light's lab where Dr. Light explains the situation and briefly how to configure their controls. The player character is a unique robot to the series (not Mega Man) created by an unknown for the purpose of watching over the events of the Tournament (by entering it), and putting a stop anything that intervenes with the event.
After the second chapter boss battle, Dr. Light is positive that Dr. Wily is behind the attacks. It turns out no one can locate Dr. Wily until the player beats chapter 4 where Dr. Light figures out where he obtained some of the parts for one of the attacking robots. After Chapter 5 Dr. Light tells the player that the police have arrested Dr. Wily, and that the player should continue the tournament anyway as they're doing so well.
Yes only does the player win the tournament, but also defeated Dr. Wily in the final battle and all the reprogrammed Robot Masters that entered the tournament. It is never explained how Dr. Wily escaped prison again (or even if the arrest actually happened) or where he was exactly hiding. The final scene shows the player robot encased in gold in an abandoned Robot Museum, where Mega Man X appears and admires the player character before the Credits roll.
The game is split up into chapters. Each chapter represents all the levels in each Mega Man game.
|1|| Mega Man? (first battle)|
|3|| Mega Man? (rematch)|
|5|| Mega Man? (final battle)|
|6|| Reprogrammed Robot Masters||Ballade|
|Genesis|| Buster Rod G ||None|
Mega Mech Shark
Police Chase+ Fake Man
Boss Rush mode
Prior to v3a, upon beating the game, a new mode is unlocked called Boss Rush mode. In this mode the player simply fought nearly all the bosses in the game without having to go through each chapter, save for Enker, Punk, Ballade and Wily Capsule. After beating all the bosses, the game's ending plays as if you beat Chapter 6. Boss Rush can be found in Auto's section of the lab.
This feature was removed in v3a, presumably because of the redesigned save feature allowing the player to jump to any point reached in the campaign, including bosses. The functionality is still in the game, however — by typing "set secret_bossrush 1" into the console before entering a boss level, the game will automatically move on to the next boss. As of v4a, all bosses after Chapter 6 are accounted for, including Duo, Buster Rod G, Mega Water S, and Hyper Storm H.