Because people found the previous version too confusing, I decided to rewrite this timeline. I've taken care to include more detail in each entry and incorporate even the latest info given to us by japanese translation and producer interviews.
Global Timeline:
MHX, the Day of Sigma || X1, The Sigma Rebellion Incident (21XX, 2114+)
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X2, The X-hunter Incident (6 months after X1)
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XC, Xtreme, The Mother Computer Hacking Incident (Many years after X was found.)
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Megamisson (3 months after X2)
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X3, The Doctor Doppler Incident (Several months after Doppler Town is founded several months after X2)
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MegaMission2, VS Revenge Limited (2 months after X3)
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MegaMission3, VS Hyper Limited
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XS, Xtreme2, The Soul Eraser Incident
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X4, The Repliforce War (Several months after X3)
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X5, The Falling Colony Incident (Several months after X4)
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X6, The Nightmare Virus Incident (Three weeks after X5)
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X7, The Red Alert Incident (Long Time after X6)
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X8, Paradise Lost
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XCM (22XX, 2202+)
Main Timeline:
20XX
-Ending to MegaMan: The Power Battle. Dr. Light has realized what robots need, they need to be able to worry, to determine right and wrong for themselves.
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20XX
-Ending to MegaMan2: The Power Fighters. The design of the girly-looking robot Zero is shown to Bass. Dr. Wily informs Bass that his energy source Bassnium used to be the most powerful energy on earth and that its creation was a mistake. Wily has learned from his mistake and given Zero an even more powerful energy source. Wily threatens that once his new creation and “that” (his other project) are completed MegaMan and Bass will be killed and the world will be his.
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20XX
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-Dr. Thomas Light is developing his greatest masterpiece, a new robot called “MegaManX”, an advanced version of MegaMan who he equipped with an ability to “worry” which marks a new epoch in robotics. X’s construction is carried out inside of an open capsule, there he is activated by Dr. Light for the first time. The doctor introduces himself and tells X that his name is a variable that represents limitless potential. Dr. Light emphasizes that X is a new type of robot which can think for himself.
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-X is once again activated by Dr. Light, he converses with him yet again, he tells X of how similar he is to humans such as Dr. Light. But, that’s also why Dr. Light is afraid that mankind isn’t quite ready to accept him. They might view X’s limitless evolutionary potential as something to be feared. He informs X that his name also carries connotations of danger. (Dr. Light has notably aged since the previous scene)
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Dr. Light has completed X and activates him one last time. He informs X that he didn’t have enough time to see X enter the world. Dr. Light says he has given X the ability to think, to worry, to grow and to evolve as he fights, but he emphasizes that it is too soon for that power to be unleashed. Dr. Light believes X will fight for justice and for hope, he tells X that he wants X to use that conscience of his to fight for the people of the future and that they will need someone like X to guide them. Saying his farewell, he closes the capsule sealing X away whilst telling him he is the world’s one true hope. (Dr. Light has notably aged since the previous scene, his health has deteriorated.)
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Having sealed away X, he leaves behind a warning message (written on September 18, 20XX) in which the people of the future are informed about X’s abilities and the dangers he may hold. He also mentions how it’s an unfortunate fact that human life is short and fleeting, meaning that he himself can not confirm the safety of the X future and there is no one to whom he can entrust his research. Thus Dr. Light has decided to seal X away hoping that someday he will be discovered in a far-flung future where he’ll fight valiantly for peace. To assure the people of the future X is not a danger he has the capsule test the reliability of X’s internal systems for 30 years. As a final reassurance, Dr. Light also urges that X is the hope of the world and of himself.
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After sealing X, Dr. Light dies, likely of old age. But before that he has also ensured to leave behind a program that will play messages for X to guide him. This program also supplies X with equipment such as armor and other upgrades. The program that plays these messages seems to have been given Dr. Light’s personality. Because of this, it can be thought that the program is actually Dr. Light brought back from the dead.
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-Dr. Wily’s greatest masterpiece Zero is under construction by him, this construction is carried out inside a capsule throughout the entire process and sometimes it involves automation using assembly line robotics. At one point during this creation process Zero is activated and he sees his creator standing ominously in front of world map. In his recollection of this scene upon his ‘death’ during the events of X5, he remarks not knowing who this person is, but he does realize that the robot that is being made is something that destroys other robots and that this robot is himself.
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-Completing Zero as much as possible (with a different design then the one he had previously shown Bass) Dr. Wily seals away Zero for the future. In doing so he gives his greatest masterpiece a mission to “destroy MegaManX”. Because Dr. Wily created Zero to be a completely evil robot, he put inside of Zero’s DNA a Virus, that would later be known as the Sigma Virus, that would awaken him to his true self.
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Dr. Wily dies, presumably of old age. However, thanks the Sigma Virus he put inside Zero he would be brought back to life in the next century.
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21XX
-Cain’s journal entry of April 8: Cain notes he has walked around searching in the wasteland for fossil proof of plants that lived in the Mesozoic Era during all of last month but nothing turned up. Hoping to find something he decides to set up camp elsewhere tomorrow.
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21XX
-Cain’s journal entry of April 9: Cain has set up camp at his new site, he laid preliminary groundwork out in a grid pattern and starting excavating. His instruments gave a strange reading on Block E-46 of this grid. A metallic substance seems to be buried several meters below the surface. Dr. Cain intends to dig there tomorrow.
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21XX
-Cain’s journal entry of April 10: Several meters below the surface Dr. Cain discovers the remains of a laboratory in ruins. At length he found writings indicating that the laboratory belonged to the famed robotics engineer Dr. Thomas Light. Looking through Dr. Light’s notes he sees that Dr. Light was making great advances and the notes keep referring to “the capsule”.
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21XX
-Cain’s journal entry of April 13:
Dr. Cain discovers the capsule. 14m tall by 8m wide, the capsule was hidden beneath a collapsed ceiling. Dr. Cain finds it odd that although the building is in rubble, the capsule alone was preserved intact. At the time Dr. Cain found it, it was running some sort of diagnostic functions. There was a warning not to touch the capsule, but all the indicators were green, which means safety. Dr. Cain concludes it’s probably okay to open it and intends to find out tomorrow.
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21XX
-Cain’s journal Entry of April 14:
After more than a 100 years of slumber X is activated by Dr. Cain, who meet each other. Dr. Cain makes note that X is a robot whose nearly human, given by Dr. Light the power to think and make his own decisions, the power of judgment. Dr. Cain concludes X is more like a human than a machine.
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21XX
-Cain’s journal entry of April 15:
Cain has tried skimming through Dr. Light’s design notes and is amazed, according to him an amazing quantum leap in robotics is described there. Using these notes Dr. Cain believes he may be able to replicate Dr. Light’s design concept to produce a new generation of robots with that design integrated into them. He intends to begin transporting X and Dr. Light’s notes back to his lab tomorrow.
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21XX
-Cain’s journal entry of November 22:
Using X as a reference Dr. Cain has completed his first “Reploid”. Dr. Cain doesn’t completely understand how the system Dr. Light built operates, but he tried to make some revisions to it. After these revisions, the Reploid became fully functional. This Reploid, who would come to be known as “Sigma” has unlimited strength and intelligence. He seems to be fully capable of making decisions and Dr. Cain was even capable of debating with it.
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21XX
-Cain’s journal entry of May 3: For the last few weeks, Reploids have been running an assembly line and shown themselves to be capable of doing even difficult tasks with ease. Dr. Cain had thus tried putting them to work with humans. The sight was rather odd, but the humans seemed to accept them gladly. (US:January 3)
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21XX
-Cain’s journal entry of July 16:
Three Reploids became “Maverick,” and were shut down because they injured two people.
This is the third case of this kind of defect in Reploids, and Dr. Cain has no idea what the cause is. Some say that they had better stop the creation of Reploid. However, Dr. Cain thinks otherwise because the humans have become too Dependant on Reploids. (US:February 16)
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21XX:
-Cain’s journal entry of November 20:
The council has had last decided to set up a countermeasure.
They’ve decided to establish a “Hunter” group to destroy Reploids that have gone Maverick before they can inflict harm on a human. The Reploid called Sigma has been appointed as the leader of the Hunters (Commander of 17th Elite Unit.) Sigma is a Reploid of the highest intelligence, one of the most intelligent Dr. Cain created and is equipped with Dr. Cain’s latest circuit design. Sigma has the talent to cope with any problem. (US: February 16, same as previous entry.)
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21XX
-Cain’s journal entry of December 10:
Sigma has been commanding the Maverick Hunters for about two years now. The actions of Sigma and his staff of Hunters have stopped Irregulars from harming humans. According to Cain it’s time everyone breathed a sigh of relief. At the same time, Dr. Cain is a bit concerned about X. X seems to lack the self-confidence to progress on the course Dr. Light planned for him. But Dr. Cain is also sure that, with time, X will find his own path in life. (US: Sigma has been commanding the Maverick Hunters for about two months now, May 16)
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-Zero is discovered and awakened from his seal by the intrusion of Reploids (Most likely Garma’s unit of Maverick Hunters) near the place in which he was sleeping. He is officially discovered in the same area where X and other ancient technology was also discovered, an area that because of this was made forbidden, giving it the name of “Forbidden Area.”
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-After wiping out Garma’s unit, Maverick Hunters succeed in cornering Zero inside of an abandoned warehouse in the Rocky Mountains. To avoid sacrificing any more men, Sigma decides to face this red Maverick by himself. During the battle, Zero tatters Sigma’s pride and self-confidence, taking great pleasure in torturing Sigma after having ripped off one of his arms in combat. Sigma eventually manages to get the upper hand by punching Zero in the head as Zero experiences a mysterious headache phenomena, displaying a “W” inside of his helmet gem. As a result of this battle the Sigma Virus transfers from Zero to Sigma. After the battle Sigma orders the red Maverick to be brought to Dr. Cain for study.
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-After Dr. Cain’s study, Zero awakens and shows no sign of Maverick behavior. Zero has miraculously transformed into a good Reploid and forgotten about his original objective to destroy X. Sigma takes Zero under his watch and Zero joins the Maverick Hunters, eventually becoming an SA-rank Hunter part of Sigma’s 17th Elite.
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21XX
-In order to help against the Mavericks, X joins the Maverick Hunters. He eventually becomes a B-class Hunter part of Sigma’s 17th Elite. X’s rank is deliberately lower than his actual abilities because of X's hesitation in battle. He becomes best friends with Zero, who is one of the few Hunters who believes in X’s ability.
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21XX
Having been infected with the Sigma Virus, a darkness began to grow in Sigma’s heart. Several months after his battle with Zero, the evil Sigma Virus’ hold on Sigma becomes complete, Sigma becomes the Sigma Virus. As a result of all this, Sigma acquired the means to start a grand scale rebellion, which he desired after witnessing X’s devotion to justice developed his philosophy of evolution.
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21XX
-Sigma calls out to rally Reploids for his rebellion in secret. After getting word of Sigma’s call to rally Reploids, Penguin went from the 13th, to directly assist Sigma more closely, joining the 17th. He was bored with life at the South Pole, his mission was a disappointment, thus he was more than willing to join Sigma.
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21XX
-The events of The Day of Sigma OVA
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21XX
-Zero is assigned to be commander of the Maverick Hunters
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-Cain’s Journal entry of July 4:
Cain reports that today, Sigma went Maverick, and took nearly all of the Hunters with him.
Cain notes that his motive is unclear, but he seems to have the false impression humans are inferior, and has pronounced “judgment” blaming humans for the arrested development of Reploids. Therefore, Sigma has decided, “Humans must be exterminated.” Cain also notes that most people are hiding, or trying to flee from the city. He doesn’t know how long humans will be able to withstand Sigma and he fears they built too many Reploids.
X diligently reports news of the fight against Sigma to Dr. Cain. He doesn’t know whether X can win or not, but he won’t stop him because something needs to be done. (US: June 4, Cain fears he built the Reploids too well. Zero has become leader of the hunters. Zero wants to go after Sigma, X is taking the news of the war very personally and wants to join him.)
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-Storm Eagle, Commander of 7th Air Cavalry, opposes Sigma's rebellion and combats him. He loses and is forced into subordination.
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-Sting Chameleon, of the 9th Special Forces Ranger Unit, opposes Sigma for his own reasons and combats him. He loses and is forced into subordination.
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-Upon receiving the word of Sigma’s rebellion, Penguin kills the commander of the 13th Unit.
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21XX
-MHX, the Day of Sigma || X1, The Sigma Rebellion Incident (21XX, 2114+)
Possible events: X’s story
Possible events: Vile’s story
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21XX
- X becomes 17th Unit commander after Zero’s sacrifice.
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-Serges revives Sigma and succeeds in building a new body for Zero. He gives Zero a new design, mostly matching the design show in Power Fighters and giving Zero his trademark Z-saber. Serges however does not have the brain chip of Zero.
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-Zero’s brain chip had miraculously survived the destruction of his body. Dr. Cain attempts to create a new body for Zero, however many parts of Zero are unanalyzable and Dr. Cain does not succeed.
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21XX
- MegaMan X2, the X-Hunter Incident (6 months after X1)
True Scenario: X recovers all parts of Zero.
Alternate Scenario: X does not recover all parts of Zero.
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21XX
-XC, Xtreme, The Mother Computer Hacking Incident. (Many years after X was found.)
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-MegaMission (3 months after X2)
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21XX
- Dr. Doppler, a reploid scientist equipped with a high performence Neuro Computer has determined the cause of the Maverick Outbreaks and created an Antivirus. Under Dr. Doppler’s guidance, the utopia of DopplerTown (Alternatively: DoppleTown/DoppelTown) is established. (Several Months after X2)
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21XX
- Doppler is corrupted by Sigma, he begins reconstruction of Vile (MK2) and builds new bodies for Sigma.
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21XX
-Doppler reconstruct his body to one equipped for combat.
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21XX
-Mavericks are revolting all over DopplerTown, Dr. Doppler’s anti-virus proves ineffective. It is thought to be a placebo because Dr. Doppler is the primary suspect of the outbreak, he has declared war on humanity.
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21XX
-MegaMan X3 (Several Months after DopplerTown is established. US: Years after X1.)
Possible Ending: Zero uses the real anti-virus from Doppler to defeat Sigma.
Possible Ending: Doppler uses his real anti-virus to defeat Sigma.
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21XX
-MegaMission2, VS Revenge Limited (2 months after X3)
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21XX
-MegaMission3, VS Hyper Limited (Shortly after MegaMission2)
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21XX
-Repliforce established (US: Repliforce v3 program established January 1)
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21XX
-Iris and Colonel are created by Repliforce scientists.
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21XX
-XS, Xtreme2, The Soul Eraser Incident
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21XX
-MegaManX4, The Repliforce War. (Several months after X3, US: Maverick outbreak, Repliforce v3 proven ineffective and potentially dangerous, June 1.)
Possible events: X’s story.
Possible events: Zero’s story.
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21XX AD
- The general of the Maverick Hunter retires out of guilt for the war with Repliforce. This person might or might not be Dr. Cain, it is a person with whiskers like General. To replace the previous general, Signas, who was designed with latest Reploid Advancements in AI (most presice CPU in existance) was urgently chosen because of his calm judgement and quick thinking.
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21XX
-Alia (high-speed CPU) is pulled from her job as researcher to become a supporter for the hunters because of her top class knowledge regarding Reploids, her designs skills in making all types of Reploids and Mechaniloids, and her excelling in program analysis and instantaneous data processing.
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21XX
-Alia analyzes the data for X's disposed armor and creates a duplicate of the Fourth Armor. This duplicate is not an exact recreation due to the materials of the original being over 100 years old, making original hard to analyze and recreate perfectly.
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21XX
-MegaManX5, The Falling Colony Incident (Several months after X4)
True Scenario: The Enigma fails, the Shuttle Operation succeeds. Zero does not go Maverick.
Alternate future event: X holds onto Zero's sword, remembering his friend. (3 years after X5)
Alternate Scenario: Eurasia crashes into earth, Zero goes Maverick.
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21XX
- The hunters are reorganized as a result of the massive losses during the Eurasia incident. All units are disbanded and all hunters are grouped together.
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21XX
-Rummaging around the wreckage of Eurasia, Gate finds a piece of Zero holding his DNA and is infected by the Sigma Virus spreading from Zero. (2 weeks after X5)
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21XX
-Gate goes Maverick and constructs High Max and the Nightmare along with other robots. He revives eight of his creations that were killed in the past because they were unanalyzable and potentially dangerous. By comparing Zero’s DNA data to the Sigma Virus he discovers startling similarities and succeeds in putting into motion Sigma’s revival program.
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21XX
-MegaManX6, The Nightmare Incident (3 weeks after X5.)
True Scenario: X and Zero team up to defeat Gate.
Future event: Zero seals himself for an intended 102 years. (After all other X-series games, tie in to the MegaMan Zero series.)
Alternate scenario: X and Zero to not meet up, X defeats Gate on his own.
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21XX
-X retires from the frontlines and helps with restoration of Earth. The Mavericks Hunter severely weakened by X's leave. Red Alert is established by Red who is 'rumored' to be formerly of Repliforce, to fill in the void left by X.
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21XX
-The criminals Aluce and Cedar obtain “Sigma Virus MK2”, they're hunted down by Red and Axl because such protection is worthless against Axl. Axl’s success in this mission attracts Sigma's attention.
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21XX
-MegaMan X7, The Red Alert Incident (Eurasia fell along time ago)
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21XX
-Colonization of the moon is well on the way: "Jakob Project." New Generation Reploids developed with special copy ability and viral immunity are developed to construct the Orbital Elevator “Jakob” at Point Galapagos. Lumine is assigned as the director. Sigma manipulates the Jakob Project to suit his needs.
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21XX
-MegaManX8, Paradise Lost.
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21XX
After Lumine’s rebellion, the production of copy/chameleon chips is put permanently on hold.
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21XX/22XX
-The production of copy/chameleon chips is restarted in the vicinity of Giga City.
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-The Orbital Elevator “Babel” is created.
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-The New Generation Reploid Redips becomes the commander of Eastern Maverick Hunter base. His abilities are hidden from the public and government, he keeps his status as a Maverick a secret.
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-X and Axl become S-class Hunters.
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22XX
-Force Metal Meteor identified in space. (2202, first half of December.)
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22XX
-Force Metal Meteor falls into the sea.
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22XX
-Giga City is created by combining research facilities and other manmade islands for the explicit purpose of mining Force Metal and Force Metal related research and development..
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22XX
-Force Metal test subjects rebel against the Federation and form the Liberion Army. (Rebellion Army)
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22XX
- Federation Goverment forms Task Force composed of Eastern Maverick Hunter Operatives under the command of Colonel Redips and sends them in to handle Liberion Army. Force Metal imbued Reploids defect, others are killed.
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22XX
-People of Giga City take matters in own hands and form the Resistance to counter the Rebellion.
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22XX
-The Federation Goverment determines Epsilon is the leader of the Rebellion
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22XX
-The Federation sends Maverick Hunters X and Zero to Giga City after realizing the need for non Force Metal imbued high-performance Reploids.
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22XX
-Mega Man X: Command Mission
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22XX
-The Federation Goverment deems Redips Maverick and postpones determination of Epsilon's Maverick Status.
Notes:
-The X7 OST mentions that the is winter creeping in after the events with Cedar and Aluce, this could be a metaphor, but also an actual seasons change.
-Axl was found after the Repliforce War, he is unaware of the event behind Red losing an eye.
-Dark Necrobat/Dark Dizzy was made by Sigma 3 years before X5 as a Maverick.
-It is unknown whether the Federation Government from XCM is the same government as in the rest of the X-series. If it is the same government, it was established in either 20XX or 21XX. If it is a new government, it is established in either 21XX or 22XX.
-Dr. Cain is born in the period between the last classic game and MHX || X1.
-Wars using robots were fought in the period between the last classic game and MHX || X1. Fighting on the side of the world government were indestructible combat robots. After the wars ended, these robots had no more use and were thus scrapped.
-The Batton M-501 model that dwells in Armored Armadillo’s stage was created 30 years before MHX || X1.