Ok get ready, it’s time to deep dive into the Yu-Gi-Oh Timelines. I’m sure you’ve read and seen many theories by now, but this one incorporates the original manga and other mangas from other series which normally have been ignored. Other stories by Kazuki Takahashi like The Dark Side of Dimensions will also be included as well as the movie, Bonds Beyond Time movie. Enjoy!
At the Beginning of Time
Numeron Dragon created the universe. It shed a tear which caused the Numeron Code to be buried on Earth.
As mankind evolved on Earth, hatred also grew. Zorc Necrophades spawned from the hatred in people’s hearts. It grew in a different dimension called the Shadow Realm.
Ten thousand years ago
The Crimson Dragon fought and sealed the Crimson Devil, Red Nova.
Five thousand years ago
The Crimson Dragon fought and sealed the Earthbound Immortals.
More than 3000 years ago
Egypt was under attack by invading armies. Atem’s father, Aknamkanon, found an ancient spellbook that could help in creating weapons - the millennium items. He told his twin brother, Aknadin, to find out a way to do it. In order to create the millennium items, it required the sacrifice of 99 souls, so the Aknadin chose a village of thieves and murders - Kul Elna. The bodies of the people who were slaughtered were melted with gold to create the 8 Millennium items, but there were two survivors from the village - Bakura and Tragoedia. These events were shown in Yu-Gi-Oh Millennium World.
The hatred of all the souls in that village helped create an evil ka, Diabound for Bakura to control. The other villager, Tragoedia, who wasn’t at the village at the time, created his own evil ka. Tragoedia was sealed by the priests using Winged Kuriboh. Unknowingly, Aknadin also summoned Zorc Necrophades to the physical plane from the Shadow Realm at the same time the Millennium Items were created. Bakura used all the millennium items to give Zorc a physical form. Atem sealed himself and Zorc in the Millennium puzzle, wiping his own memory in the process. However, Zorc also put a fragment of his soul into the Millennium Ring.
Shadi and his ancestors guarded the 8 Millennium items for 3000 years until he gave the Millennium eye to Pegasus. Bakura touched the Millennium ring, turning him into Yami Bakura (Bakura influenced by Zorc’s soul) and murdered Shadi. Aigami and his sister, Sera, who were orphans adopted by Shadi, witnessed this and were given the 8th Millennium item, the Quantum Cube by Shadi before he died.
1960s (3000 Years later)
Solomon Muto (Yugi’s grandfather), finds the Millennium Puzzle in the Tomb of the Nameless Pharaoh (Atem). The first Yu-Gi-Oh manga series followed by Yu-Gi-Oh Duelist begins (Duel Monsters). Atem defeats Yami Marik at Battle City, freeing Yami Bakura from the Shadow realm.
Before Yugi and Atem’s Ceremonial Duel, Bakura removes Pegasus’s Millennium Eye, killing him in the process. (This was shown different in the anime where Pegasus lives. However, we know from the Dark Side of Dimensions, that Pegasus is nowhere to be found, confirming Pegasus’s death.) This leads Pegasus’s twin sons to seek revenge for their father’s death. Yu-Gi-Oh R and the Wicked Gods arc begins. After that, the final events of Yu-Gi-Oh Millennium World occur with the Ceremonial Duel and Atem goes back to his world.
Note that in this case, it is clear cut that the manga is canon because it came before the anime and Kazuki Takahashi wrote it. The Dark Side of Dimensions, also written by Kazuki, is consistent with the manga not the anime with the main difference being Pegasus’s death.
The Yu-Gi-Oh GX manga occurs here. The tomb of Tragoedia was opened by archaeologists which allowed Traogedia’s spirit to possess them and body hop until he landed inside Mr. Phoenix (Aster Phoenix’s father). He created his own deck - the Legendary Planets archetype. Eventually, the current World champion - Koyo Hibiki, dueled Traogedia and lost, putting a curse upon him that each time he would draw a card, his heart would weaken. He met Jaden at the hospital and taught him everything he knew about dueling. He had his last duel against Jaden where he won, but then fell into coma. He gave his hero deck to Jaden along with the card, Winged Kuriboh. The events of Yu-Gi-Oh GX occur. Jaden and Chazz team up together using Winged Kuriboh and Light and Darkness Dragon to Fusion Summon, Ma’at, who has 7 Millennium items. Tragoedia is defeated. Koyo Hibiki wakes up from coma. Jaden later graduates from Duel Academy.
The Yu-Gi-Oh GX anime premiered in 2003 on TV Tokyo. It was considered a spin-off and not written by Kazuki Takahashi. The first 156 episodes were written by Junki Takegami. Episodes 157-180 were written by Shin Yoshida. The GX manga, on the other hand, was written by Naoyuki Kageyama and it was published in 2005, 2 years after the GX anime. Hence, one can argue that they are two completely separate continuities. One of the main differences was that the manga explained who gave Jaden his hero deck and the significance of Winged Kuriboh. In the anime, Yugi gave Jaden his Winged Kuriboh who became Jaden’s friend throughout the series but was never used for anything significant. Rather, in the manga, Winged Kuriboh was required to defeat Tragoedia who was sealed using Winged Kuriboh millennia ago. It’s hard for the GX manga and anime to co-occur without overlap and contradiction. Hence, here one can say that they are two separate continuities or say that the manga fills gaps where the anime does not explain.
Following this, is the Dark Side of Dimensions movie which is logically consistent as the sequel to the Yu-Gi-Oh manga following the Ceremonial Duel. Atem defeats Aigami.
Everything we’ve discussed so far until this point has been straightforward. Now comes the hard part which involves timeline splitting.
17 years Prior to Yu-Gi-Oh 5D’s
The original story continues with KaibaCorp. advancing technology of Solid Vision holograms. A branch of KaibaCorp, Reactor Research Division (R.R.D.), did research on energy. Eventually, Dr. Fudo, one of the leading researchers, discovered the “Yusei Ryushi”, a planetary gear that binds particles together through strong bonds. A combination of these gears allowed each gear to help spin the other gear, allowing all gears to spin forever without any energy input. Using this technology, he was able to develop the Ener-D, a perpetual motion machine, that gave Neo Domino City virtually a limitless amount of energy. Dr. Fudo named his son, Yusei after the gear. The first designs of Synchro monsters emerged and were released to the public. It was found that using Synchros caused Ener-D to spin faster speeding up human evolution. Things were pretty good.
200 Years later
Having an unlimited supply of energy, people abused the power of Ener-D to the point where they were corrupted with greed and desire. More Synchro Summoning made the Ener-D spin faster. Since Ener-D was made-up of small Yusei gears, these gears were also self-aware and sentient. They had the ability to read the thoughts of human beings. The negative emotions of the human population influenced the Ener-D to deem humanity as unworthy. It created the Meklord Emperors with the directive to wipe out all humanity. This led to the Meklord Emperor Genocide.
In this timeline, Dr. Fudo’s son, Yusei fought the Meklord Emperors. He learned by removing all the negative emotions of hatred and greed within him, he can create a state of mind called “Clear Mind”, which will stop the Meklord Emperors. However, Yusei eventually died and was unsuccessful to defeat the Meklord Emperors alone.
A scientist named Z-One took inspiration from Yusei and in order to teach humanity about Clear Mind, he used plastic surgery to change his face to like Yusei Fudo to give people hope. However, it was not enough to quell the negative emotions in the human population. Ener-D kept rotating faster and faster, gaining more momentum with more negative emotions and the use of Synchro Summoning. This caused it to spin so fast, shifting into reverse, and exploded, called “Zero Reverse”. There were only four survivors - Z-One, Aporia, Antimony, and Paradox. Eventually only Z-One was the survivor.
Z-one creates other cyborgs in the images of his friends - Paradox, Antimony, and Aporia. Eventually Z-One builds a time machine. He sends each of them back to the past at different points in an effort to prevent the creation of Ener-D and the extinction of humanity. (It’s almost like Terminator where he’s sending people back to prevent Skynet.) He first sent Aporia, Antimony, and himself back in time prior to the creation of Ener-D. In that point of time, KaibaCorp. is still exists. He secretly manipulates events behind the scenes and creates the organization known as Iliaster.
Here, begins Yu-Gi-Oh 5Ds. Iliaster made sure that Roman Goodwin is in charge of development alongside Dr. Fudo. Before Ener-D is completed, Roman intentionally overloaded the Ener-D reactor, causing it to explode. This killed several people including Kaiba, Yugi, Joey, Tea, Yusei’s parents, Jack’s parents, Crow’s parents, etc. However, with the Ener-D destroyed, it prevented the Meklord Emperor Genocide in the future, or so Iliaster thought anyways.
The ruins of the explosion become Satellite city. Note that not a lot of time has passed since GX since a character named Tetsu Grudge is still alive who was present in Duel Monsters. He is an adult now, a cop whereas in Duel Monsters, he was a teenager. Likely 20-30 years have passed.
A new Ener-D was created within Neo Domino City. Hence, Iliaster was unsuccessful. Aporia and Antimony were eventually defeated. Z-One tried to use his lab, the Divine Temple (another Ener-D reactor), to crash into Neo Domino City’s Ener-D reactor, in an effort to destroy both reactors. Yusei defeated Z-One. In the process of Z-one explaining to Yusei what happens in the future, little did he know that everyone was listening. This caused humanity to change their perspective and be wary of having negative emotions like greed and hatred. Z-one realized this and upon his defeat, crashed himself into the Divine Temple before it could crash into Neo Domino City, saving it.
Paradox, unlike, the others, was sent back even further back in time as a backup plan in case Z-one were to fail. The time point Paradox chose was before Atem and Yugi’s Ceremonial Duel. Paradox blamed Duel Monsters, the card game, as the primary reason for Ener-D speeding up. Hence, his mission was to kill Pegasus and prevent the creation of Duel Monsters. However, instead of simply killing Pegasus and erasing Duel Monsters from history, he went about it in a different way. He instead chose to kill Pegasus at a public event to scare the populace into thinking Duel Monsters is the cause. Paradox’s idea was to remove Duel Monster’s influence from history so that people would learn not to recreate anything like Duel Monsters ever again. Paradox succeeded in killing Pegasus and Yugi’s grandpa. It is also possible that he killed Kaiba to prevent KaibaCorp. from researching the Ener-D. We see Paradox use the Malefic Blue-Eyes White Dragon which is proof that he must have encountered Kaiba. The Crimson Dragon sensed a distortion in time, and sent Yusei back in time to fight Paradox. This is where the Bonds Beyond Time movie takes place.
There is again a Yu-Gi-Oh 5D’s manga and anime. The manga is a spin-off off the anime and does not include anything about Iliaster. Rather, the manga ends with the defeat of Rex Goodwin and then goes to a 1-year time skip to a 2nd World Grand Prix. Hence, we can regard these as separate continuities again. The 5D’s anime is still much more complete than the manga. Regardless, Paradox caused splitting of the timeline into one where Paradox was defeated and one where he succeeded.
Timeline where Paradox succeeded (Zexal)
In the one where he succeeded in killing Pegasus, he created a new timeline without Synchros. This new timeline was Yu-Gi-Oh Zexal. We see statues of Dark Magician, Blue-Eyes White Dragon to confirm that this isn’t a continuity completely in isolation from Duel Monsters. The only time we ever see or hear Synchro Monsters is in a gag manga, which is a spin-off of the actual Zexal manga, D Team. A girl named Syndy Chross (her first name a pun on Synchro), uses them.1 So we can explain this in two possible ways - one is to simply discount this gag manga and the other is to state that she was the only person with a Synchro deck because she was one of the descendants of the designers of Synchro monsters that never got released to the public since Pegasus and KaibaCorp. were destroyed.
Timeline where Paradox failed (Arc-V)
In the scenario where Paradox was defeated, everything happens as normal with the first Ener-D exploding and leading to 5Ds. Years after 5Ds, and after Yusei defeated Z-One, Astral came to Earth and the Xyzs cards also were a thing but this Zexal was different from the one in the anime. Synchro and Xyz hence both existed. Several years later, a boy named Z-arc, was a very powerful duelist who became selfish and greedy for power. He thought by hurting people during the duel, the audience would cheer for him more. He eventually fused himself with four dragons to become the Supreme King Z-arc. He was causing destruction everywhere, so Ray Akaba, a girl, used four cards, to split Z-arc into four boys, by doing so, it also caused splitting of the Original Dimension into four dimensions - Synchro, Xyz, Fusion, and Standard. Memories of this event were wiped so nobody realized their dimension was once fused with Standard.
Z-arc’s desire to stay united clashed with Ray’s desire to stay divided. That is, it could not decide whether reality should swing one way or the other (like a pendulum). This led to the creation of a pendant that Yuya wore but reacted to his other personalities - Yuto, Yuri, and Yugo. Eventually, Yuya’s pendant was able to transform effect monsters into the new, Pendulum monsters.
10 Years Before V-RAINS
10 years ago before the start of Vrains, there was the Hanoi Project. The project that resulted in the creation of Ignis, the AI. Here, Pendulum monsters are nowhere to be seen, indicating that this timeline likely follows after Zexal. Yugioh sevens will now continue in another timeline before Synchros, Xyz, Pendulum, or Link.
Yu-Gi-Oh Vrains begins and ends.
The new series is difficult to place given the absence of Synchros, Pendulums, or Link monsters. Rather it seems like a reboot of the series and has a completely different format. Instead of KaibaCorp., Goha is the new corporation. It’s possible that this does take place in the timeline where Paradox succeeded in killing Pegasus and Kaiba, which would halt the progress of new Summoning mechanics and also destroy KaibaCorp. Thus, Sevens could be a prequel to the Zexal series, before Astral came to Earth, explaining any absence of Xyz monsters.
And that’s it folks. This is just a theory so far.