Megaman's back on a whole new adventure.

One year after the Kattelox incident, Megaman's life once again returned to normal. However, all of that changed when Roll saw a woman on the TV that looked a lot like her mother. That same woman attacked the ship Professor Barrell & his friend, Professor Verner von Bleucher was on. The ship sank to Forbidden Island. Megaman went on a mission to save them, but met an ancient girl named Sera on the way. Her servant, Geetz, says that they need the Mother Lode in order to save Sera's life. In return, the Mother Lode will provide limitless amount of power. Knowing this, and with the hope of uncovering the mystery behind Roll's parents, Megaman braves a whole new adventure in search of the Mother Lode. However, on his way, he learns something about his past as well.

Depressed at the thought that Professor Verner von Bleucher will find the Mother Lode before her, Roll mopes around the Flutter. Megaman, in an attempt to cheer her up, turned on the TV for Roll. Roll was shocked at what she saw, her mother! Or a woman that looks a lot like her. Seeing this, Roll is determined to find out if her parents are still alive.

Spoiler: Data now reveals Megaman's past. He was once a Purifier Unit. He was under the direct service of the Master, the last true human. During that time, the number of humans was dangerousy low. The master, the last human remaining, used the DNA of the previous humans and created clones called "Beta". The more advanced Betas were called "carbons". Being the last human, the Master is lonely, and requested Megaman by his side. He and Megaman lived at Elysium, another planet, for 3000 years. The Master cannot live Elysium because without Elysium's life support system, he will die. However, the Master requested to be brought to Terra, planet of the carbons, so that he may experience how the carbons lived. Megaman and the Master landed on Calbania Island. He then realized that the carbons are not just mere clones, but they are also people. Only after a few minutes, the Master died. But before he died, he requested that Megaman should destroy Elysium. Because when the last human dies, Elysium will activate the Carbon Reinitialization Program, which will destroy every carbon and create new clones using the last human's DNA, that Megaman currently possesses. Megaman tried to destroy Elysium but every other unit under the Elysium's command tried to destroy Megaman. Megaman retreated back to Terra, while Sera & Yuna, Mother Units, followed. Sera battled Megaman but without Elysium's system, she was severely damaged. Megaman was also fatally damaged due to the battle. Yuna realized that what Megaman was doing is under the Master's command, and took a neutral stand, neither helping nor fighting. After seeing the 2 units severly damaged, She locked both units inside Crystals. The Carbon Reinitialization Program cannot operate without Sera, so the carbons continued to evolve, forgetting everything about Elysium & the Master.

Barrell was invited by his old friend, Verner von Bleucher, to go on an expedition into forbidden island. Many years ago, they both tried to enter Forbidden Island, but lost consiousness half way. They awoke outside town. 10 years ago, Barrell's daughter and son-in-law decided to pick up where Barrell failed, and enter Forbidden Island. They left Roll, their only child under Barrell's care.

Spoiler: 15 years ago, Barrell entered the Nino Island ruins without permission from the Guildmaster. Before he even went through the first door, he saw a crystal. The crystal spinned really fast until it broke. Out came a baby and a little robot monkey. Fearing that if he told everyone about the baby, his Digger's license would be taken away for entering the ruins without permission. So he decided to adopt the baby. he raised it along with his granddaughter, Roll. Roll gave him the name Megaman, after her favorite video game character.

Verner von Bleucher is a wealthy man. He created the Sulphur Bottom, an impenetrable ship, with one purpose, to discover the mystery of Forbidden Island. He believes that the Mother Lode resides in the center of that island.

Glyde is a pirate. However, he is not all talk. He has the mecha & the skills to back it up. Unlike the Bonne family, he works alone.

The Birdbots are abnoxious, dishonest, rude little robots. However, they are hard workers and good fighters. They are under the command of Glyde

Bola & Klaymoor are very skilled diggers. Klaymoor wants to obtain the Mother Lode while Bola is only forced to come along. Bola is laidback and easy going and specializes with blades. Klaymoor is hardcored and determined and operated a rapid-fire buster.

After the Kattelox incident, Teisel sold the rainbow refractor he got and started a department store business. However, it went bankrupt because of Teisel's lousy judgement. With no other choice, and drawn by old habits, he returned to pirating. And his first target, the Mother Lode.

Bon is the same as before. The only difference is he can change his armor. And he's a lot more stronger now.

Tron is the same as before. Only now she become more cunning at dealing with her enemies. She is also more open with her feelings with Megaman

41 servbots who each have different specialties and personalities that happily and clumsily serve the Bonne family in any way they can and will do anything for Tron even going as far as asking Megaman to join them as the 42nd servbot. Need I say more?

Matilda disquised herself as a reporter and warned the people about the Mother Lode. She said "What you call the Mother Lode is not what you think it might be! No, it's not a treasure at all--it's a catastrophe waiting to happen!"