The Carbon Reinitialization Program

The Carbon Reinitialization Program, known (roughly) as the "Humanity Regeneration Program" (人類再生プログラム Jinrui Saisei Puroguramu) in Japan, is a program of the Master System that was meant to be run only after the Master and all other humans have died, using their genetic code that was stored in Elysium's Library to clone new humans and "delete" all Carbons (humans) on Terra, restoring the Ancients.

In Mega Man Legends 2, the Carbon Reinitialization Program of Elysium could only be accessed by putting the four keys of "the Mother Lode" in their right places for the door to the Mother Zone Library, which contains the genetic records of the humans who built the System. Yuna had hidden the keys after Mega Man Trigger and Sera's battle thousands of years in the past, so Sera could not start the program. In the present time Sera and Geetz convinced Verner Von Bluecher to enlist Mega Man Volnutt and Roll Caskett to search for the keys, telling them that they are needed to unlock the Mother Lode and have access to technology that has long been lost.

It was the Master's last wish for Mega Man Trigger to delete all data from the Library and destroy the Master System. By the end of Mega Man Legends 2, Mega Man is able to permanently shut down the Carbon Reinitialization Program as well as the Master System.

In Mega Man Legends, Mega Man Juno attempted to use a reinitialization program similar to the Carbon Reinitialization Program, but that would only reinitialize the Carbons on Kattelox Island instead of the entirety of the planet. This reinitialization program was intended to keep the Carbons on Kattelox Island from overpopulating and is supposed to be activated every one-hundred years.

In the crossover game Namco × Capcom, Juno was revived and became an "Aberrant Unit" that tries to reinitialize all Carbons on the planet with Eden.

The history of the Carbon Reinitialization Program
Many thousands of years in the past, the Master System was created along with the artificial humans known as Carbons. It is unknown exactly who created the Master System and the Carbons, but they were both possibly the creation of The Master. The Carbon Reinitialization Program was created as a part of this program in the case that the Master and all of the other humans were to die, they would be resurrected with their genetic codes which were stored in the Library of Elysium. Once the Carbon Reinitialization Program is run, all Carbons on Terra would be wiped out and replaced with the newly cloned original humans. This would be done through a series of satellite-like space stations that are scattered around Terra that would launch explosive devices to wipe out all of the Carbons

In his former life, Mega Man Volnutt—then known as Mega Man Trigger—was asked by The Master to destroy the Master System and to save the Carbons of Terra. Mega Man, attempting to fulfill The Master's dying wishes, turns against the System and tries to put an end it to before the Carbon Reinitialization Program can be activated.

The Mother Unit, Mistress Sera, defends the Master System from Mega Man and travels to Terra to stop him from destroying it. The two of them battle to the point where they expend all of their energy. At that point, the Mother Unit, Mistress Yuna takes the opportunity to seal them both away in stasis fields. Sera is sealed away along with her Servitor Unit, Geetz, and Mega Man is reset to his original configuration, becoming a child again, and is sealed, along with the robot monkey that he created to store his memories, in the Nino Island ruins.

These events eventually become known as the story of the two Goddesses of the Earth and the Sky and the rumor of the Legendary Mother Lode.

Thousands of years pass and eventually the planet is covered by endless water. Some people who are recognized as being Diggers that search the Underground Ruins of the ancient civilizations for treasure begin to whisper between each other about a legendary treasure. This legendary treasure is eventually known as The Mother Lode. The Mother Lode is describe as a treasure and an energy source so great, that the world need never fear of running out of the energy, with many Diggers searching for the treasure for their own reasons, such as money or fame.

Finding this treasure becomes the ultimate goal of many Diggers around the world, However, the treasure is actually the lost story, altered through time, of the Carbon Reinitialization program.

The search for the Mother Lode/The Carbon Reinitialization Program
A famous Digger and scholar, Barrell Caskett, and a long-time friend of his, millionaire Verner Von Bluecher, go on a search for the Mother Lode. This search leads them to a mysterious island where all who visit never return. This island is known as Forbidden Island.

While on Forbidden Island, the two lose consciousness, with Barrell only remembering seeing a young woman before him as he passes out. This young woman was Yuna who is still guarding the island in order to keep anyone from finding Sera. When Barrell and Bluecher regain consciousness, they find themselves on the neighboring continent of Yosyonke, unsure of how they survived and wound up there. Unbeknownst to them, Yuna had rescued them.

Many years later, Barrell's daughter Matilda and her husband Banner, inspired by stories the she was told by her father of his adventure to Forbidden Island, decide to venture there themselves. Leaving their daughter Roll behind with a neighbor and leaving a letter addressed to her father Barrell, Matilda and her husband Banner begin their adventure to Forbidden Island. Banner has created a specific machine to enter through the storms that surround Forbidden Island called a Dropship and they use it to land on the Island.

While on the island, they are unable to cope with the harsh environment there and eventually succumb and lose consciousness. Yuna finds them, and is able to rescue Banner by sending him back to the continent of Yosyonke. However, Matilda is too badly injured and Yuna has no choice but to use the nanotechnologies from her body and her own energy to save Matilda. Now having expended too much of her own energy to save Matilda and being unable to move herself, she has to occupy Matilda's body until her own body is repaired enough to be usable again. Yuna stores her body in the Dropship that Matilda and Banner used to enter Forbidden Island and continues to watch over Sera. Matilda and Banner are never heard from again and are considered to be missing.

In the present time, Mega Man Volnutt and Roll Caskett are searching for the legendary Mother Lode in the hopes that it will lead them to find Roll's parents.

While on their search for the Mother Lode, they wind up trapped on Kattelox Island after the Flutter breaks down. While there, they eventually explore the Underground Ruins and the Sub-Gates of Kattelox Island which lead them to the Sub-Cities of Kattelox and the Main Gate. When Mega Man reaches the bottom of the Main Gate, he encounters the Bureaucratic Model Mega Man Juno. Mega Man Juno makes references to the Carbon Reinitialization Program, threatening to wipe out the Carbons of Kattelox Island and reset the population there. After stopping Mega Man Juno and preventing Eden from destroying Kattelox Island, they leave Kattelox Island and continue their adventure to find the Mother Lode, without the knowledge that the Carbon Reinitialization Program that Mega Man Juno had referenced is the treasure that they are searching for.

The search for the keys to the Mother Lode
As Mega Man Volnutt and Roll Caskett continue to search for the Mother Lode, Verner Von Bluecher invites his old friend Barrell to accompany him on a second trip to Forbidden Island. This time, Bluecher is flying there in his newly built enormous flying machine—the Sulphur Bottom. Barrell joins him, and the two fly close to the island, only to be confronted by Yuna (inside of Matilda's body) before they can pass through the storm. Yuna telling them that what they know as "The Mother Lode" is not a treasure at all, but a catastrophe waiting to happen. In a skirmish with Yuna, the Sulphur Bottom is damaged and is lost in the storm above Forbidden Island.

Mega Man and Roll, having watched this happen on the television, decide to venture to Forbidden Island themselves in order to save Barrell.

Mega Man, eventually using Joe's (Banner's) newly built Dropship to land on Forbidden Island somewhat safely, reaches the center of the island only to discover that the presumed Mother Lode that was hidden there is actually Sera, still locked away in the stasis field that Yuna trapped her in.

After Mega Man releases Sera from the stasis field, she tells them that in order to find the Mother Lode they are searching for, they must find four keys. These keys are known as the Keys to the Mother Lode. She is able to deceive Mega Man, Roll, Barrell, and Bluecher into searching for these keys in many ruins around the world.

Sera gives them the location of the first key in the Manda Island Ruins, which Mega Man retrieves after fighting with the Air Pirate, Bola, and defeating the Gargarfummi Reaverbot.

Sera then tells them that the second key to the Mother Lode is located in the Nino Island Ruins where Mega Man was originally discovered by Barrell. Mega Man is eventually able to retrieve it after defeating the Midosu Reaverbots and fighting with the Air Pirate, Klaymoor.

They are told by Sera that the third key to the Mother Lode will be found in the Saul Kada Ruins. After fighting the Bonnes throughout the ruin and defeating the Wojigairon Reaverbot, eventually concluding by chasing Bon Bonne who was able to steal the key, he is able to retrieve the third key.

They are then told by Sera that the fourth and final key to the Mother Lode is hidden within the Yosyonke Ruins. After defeating the Air Pirate Alliance that consisted of the Bonnes, the Glyde Family, and temporarily Bola and Klaymoor, Mega Man is able to enter the Yosyonke ruins in order to search for the fourth key. Mega Man is eventually able to locate the final key to the Mother Lode and is subsequently attacked by the Rimblemenji Reaverbot. He is able to defeat the Rimblemenji Reaverbot and return to the surface with the fourth and final key.

After collecting all four of the Keys to the Mother Lode, Mega Man returns to the Sulphur Bottom where Sera is waiting for them. Everyone is questioning what will happen now that they have collected all four of the keys and if it will really lead them to the Mother Lode.

The keys begin to light up and Sera and Geetz attack everyone aboard the Sulphur Bottom, Geetz having hacked into the Sulphur Bottom's computer system. Above the deck of the Sulphur Bottom, Geetz and Gatz engage in a battle. Gatz is defeated and Mega Man reaches the deck of the Sulphur Bottom to confront Geetz. Mega Man and Geetz begin to battle on top of the Sulphur Bottom with Mega Man eventually able to gain the upper hand on Geetz and defeat him. However, Geetz throws one last attack at Mega Man by sacrificing himself in a self-destructive explosive attack in an attempt to take Mega Man's life before he can confront Sera.

Mega Man, being hurt to the point of nearly dying and becoming comatose, begins to have dreams and visions of Sera, Yuna, and his memories of The Master and his former life eventually return to him.

After Mega Man regains consciousness, and finds himself in a room in the Sulphur Bottom. Roll asks him if he is alright. Yuna explains that they have used the backup data that was stored in Data in the case that something happened to Mega Man or his memories.

Yuna explains that Sera now has the four Keys to the Mother Lode, which has now been revealed to be the keys to activate the true Carbon Reinitialization Program. She plans on activating the program and wiping out all of the Carbons on Terra. Mega Man now remembers that the final request of The Master was for him to destroy the Master System and prevent the Carbon Reinitialization Program from ever taking place and to protect his Genetic code from the Master System.

Mega Man, now faced with the decision to either obey the system that the Ancients created and carry out the Carbon Reinitialization Program or fulfill The Master's dying request to terminate it permanently, wonders what he should do.

Roll then tells Mega Man that she trusts his judgment on what to do and that they will do it together.

Mega Man then makes the decision to take The Master's Shuttle Pod with Yuna to return to Elysium and face Sera.

Once they reach the Shuttle Bay on Elysium, Mega Man has to make his way through the Defense Zone and eventually reaches the Residential Zone. After he finds the Master's old house, he then makes his way through the Mother Zone and past the several Boss Reaverbots that defend it.

Mega Man eventually makes it to the Library where the Ancients' genetic code is stored, awaiting to be revived after the Carbon Reinitialization Program is completed.

Mega Man then enters the room where he discovers that the Carbon Reinitialization Program has been paused and is awaiting further instruction from the Mother Unit. Mega Man is confused, and Sera appears before him. Sera wants to fight and defeat Mega Man before she activates the Carbon Reinitialization Program.

Mega Man and Sera fight until they wind up in the sky of Elysium where Sera transforms into her final form. After one final battle, Mega Man is finally able to defeat Sera and stop her from activating the Carbon Reinitialization Program.

After Mega Man ends the battle with Sera, the Carbon Reinitialization program has been permanently shut down along with the entirety of the Master System. Yuna appears to explain that with the Master System now gone, the old System that The Master's people shut down—which the Master System had replaced thousands of years ago at its creation—has begun activating again throughout Terra. Yuna explains that the underground labyrinths that the Carbons know as the "Underground Ruins" are the many remnants of this old System that are reactivating now.

Unfortunately, Mega Man, Yuna, and Sera who is now inside Yuna's original body are trapped on Elysium with no way to return to Terra to protect it from the Elder System's reactivation.

Mega Man then tells them that there is nothing to worry about because Roll will come looking for them no matter happens.