Shin Mazinger ZERO vs. Great General of Darkness (Shin Mazinger ZERO versus Ankoku Daishogun, 真マジンガーZEROvs暗黒大将軍) is a sequel to Shin Mazinger ZERO that began on February 2013 and ended on November 2015. While the previous manga was a remake of the Mazinger Z series, this manga is based off the short but notable film, Mazinger Z vs Great General of Darkness. It introduces the Great Mazinger as a major plot element.
With the defeat of Dr. Hell, the Photon Power Laboratory and its allies are living out their days in peace. Minerva X is relieved that Mazinger Z managed to avoid its fate of becoming a Majin. However, trouble boils up across different parts of the world and a prophet appears telling Koji Kabuto and his friends about an evil that could consume the world. Soon the Mycenae Empire rises to retake the surface and annihilate the present civilization and any other threat. Effortlessly taking out robots of the World Nations, even Mazinger Z (with Koji in a now restored flesh and blood state) is overpowered until the arrival of the Great Mazinger created by an alternate reality's Kenzo Kabuto who is also revealed to be the prophet from before.
Kenzo had come into the present world during the battle against Dr. Hell that bent time and space which caused different realities to fuse together including the one where Dr. Kabuto and the Mycenae Empire came from. With the Great in tow, Dr. Kabuto just needed a suitable pilot to combat the Empire. He requested that the Photon Lab not release Mazinger for exactly 24 hours in order to get the pilot ready. Unfortunately, the Empire broke through the lab's defenses and several people including Prof. Yumi and Boss lost their lives. When Mazinger Z mobilized it was completely overpowered by the empire's weaponry, which was capable of damaging Super Alloy Z. The Great General of Darkness himself then appeared to claim victory
Although training and tuning were unfinished, Dr. Kabuto launched Great Mazinger with its pilot Tetsuya Tsurugi. The Great's Super Alloy New Z and weaponry managed to put up a greater defense against the Warrior Beasts. Later the Great faced against the Great General. During the battle, Mazinger Z began to resonate with the Great Mazinger and Tetsuya's emotions driving it out of Koji's control. With this, Z unleashed its seventh black box 'Majin Change' awakening the Majin from previous realities, Mazinger ZERO.
The Great faces against Mazinger ZERO in battle. Sayaka and Minerva then manage to contact Koji and Tetsuya through Mazinger's virtual space telling him to find a way to break the loop. As Tetsuya discussed a strategy with the girls; Great Mazinger then transforms into its more powerful form, Great Mazinkaiser. The Great General also enters battle allowing for a temporary alliance to fight this enemy. Unfortunately ZERO overpowers the Kaiser using its Breast Fire but the Great manages to grasp onto ZERO's canopy for Minerva to use the Rust Hurricane in order to send Koji back in time to a different reality with Koji promising never to forget them as he dissolves into photons.
Minerva awakens in a different world one where Great Mazinger and the Mycenae Empire are locked in combat and Koji and Mazinger Z are nowhere to be found. It is revealed that in this reality Tetsuya is actually a series of clones created to pilot the Great Mazinger as many who have tested the Super Robot including Dr. Kabuto himself was either critically injured or killed from the Great's immense G-Force. This causes concern for Tetsuya's partner Jun Hono who started to grow feelings for Tetsuya and witnessed the death of many clones. Minerva gathers information including Koji's location where he is working with NASA's TFO lab and (to the anger of Sayaka and Minerva for forgetting his promise) is in a fake marriage to Maria Fleed to obtain technology to locate Mazinger Z. Maria in turn is keeping an eye on Koji under directions from her older brother Daisuke.
Using the technology of the TFO lab, Koji manages to enter the dimensional boundaries where the Mycenae Empire is hiding revealing that Mazinger Z is in their custody and is sealed. As battles with the empire become more intense with yet another clone of Tetsuya dead, Koji prepares to reenter battle putting on his old pilot suit in spite of some concerns from his loved ones who have decided to put their faith in him. Koji and Tetsuya come across Dr. Hell who in this reality had survived the battle with Z and was actually sent back in time, conquering Bardos while acting as the Emperor of Darkness. Koji manages to free Mazinger and fight against Dr. Hell as the emperor uses the robotic body the Great Marshall of Hell to battle Z while Great battles the Great General of Darkness. Z seems to have won but Koji is ejected from the body and Dr. Hell takes over the body forcing Mazinger into an altered ZERO form revealing that Dr. Hell is a clone of Koji's grandfather, Juzo. Great Mazinger manages to defeat the Great General but is effortlessly defeated by Dr. Hell. With yet another hopeless situation before them, Minerva with Koji's request sends Koji's soul to another reality.
The next realities however have a very stark difference between them with Koji deciding to imprison himself to prevent Mazinger ZERO from awakening while making himself look like a criminal. A visit from another Koji however reveals how ZERO can still appear through different realities as its own entity and how it influences other realities. Koji with the Reality Manipulation of the Mazin Power black box, combines the alternate realities into a singular universe. The setting changes again where Mazinger Z is merely a media icon throughout the world (and the only mecha series in general) after his grandfather and father develop the robot as a toy. Koji lives a normal life with his family (including his now living parents and grandfather) and classmates until he encounters Tetsuya. Tetsuya is on borrowed time as he does not exist in this reality reminds Koji that although Koji might not do anything, the threat of ZERO still exists and would only repeat itself until action is taken.
Koji uses the reality manipulation ability to revive Tetsuya and construct Mazinger Z and Great Mazinger to fight the embodiment of ZERO itself. Their attacks do not do much to affect it but Koji uses Photon Energy to bring people's ideas of other robots in the form of other Super Robots including Grendizer, Getter Robo, and Steel Jeeg. Soon even more spirits appeared in the form of other mecha (including the first Gundam (RX-78-2 Gundam), Gunbuster, Eva-1, and many more). The combined power completely overwhelms ZERO. ZERO in its last moments claims of Mazinger falling into obscurity and be forgotten. But Koji does not mind as long as the memories of his friends and loved ones remain along with the never-ending possibilities that are available. With ZERO realizing that those other realities existed because of Mazinger, it accepts its fate as it is destroyed. ZERO's destruction causes an event horizon that recreates the universe with the sun's light shining on Earth's surface in a new reality.