In the year 21XX, a doctor by the name of Dr. Cain was on a digging expedition in an area of a new forest area where he discovered the lab of the famous robotic inventor of 20XX , Dr. Thomas Light. After some excavating, Dr. Cain discovered a capsule that contained what Dr. Light called a reploid. Inside was the first reploid created, Mega Man X. According to the message left by Dr. Light, "X" is the first the first of a generation of anew innovation, the ability to think, feel and to make their own decisions. However, if X were to break the first law of robotics, "A robot must never harm a human being", the results would be disastrous. Dr. Light sealed X within a capsule for 30 years or so while running systems that would determine the reliability of X. Dr. Cain was witness to the awakening of X.
Dr. Cain was able to comprehend the plans of a reploid and soon mass production of reploids began. Soon reploids were a common site. Development of new organizations began, like the Repliforce. However, some reploids started to attack humans. These 'Mavericks' were becoming more frequent and Dr. Cain and a few others organized the 'Maverick Hunters', a group of reploids and few humans to hunt down the Mavericks. The Maverick Hunters were small at this time, consisting of a least four units. The leader was a reploid known as Sigma. Along with his unit of 8 reploids, they were able to control the Mavericks. X in the meantime was trying to live a peaceful life.
Soon, however, Sigma began to act strangely and without warning, he and other Hunters went Maverick. This was the start of the First Maverick War. The Maverick Hunters received a new leader, a mysterious reploid known as Zero. X also started to fight the Mavericks.
While Zero was gathering information on Sigma's new fortress, X went to take out the 8 Mavericks that stationed themselves in the area. With the help of capsules that were left for X by Dr. Light, X was able to destroy the Mavericks and was able to join Zero on the attack of Sigma's base. A Maverick called Vile was able to capture Zero and X wasn't able to defeat his ride armor. Zero was able to destroy the armor, but at the cost of himself. X was able to destroy Vile, but was too late to save Zero. X soon made his way to Sigma and was able to destroy his pet reploid dog, and Sigma's two forms.

The First Maverick War was over, but the Maverick Hunters had a lot to do. X assumed command of the new 17th Unit of the Maverick Hunters and was able to track down the few Mavericks that remained. While X was able to stop these Mavericks, a group who called themselves the "X-Hunters" claimed to have the key parts of Zero and X would have to destroy them to regain them. X was able to retrieve these pieces and to destroy the Mavericks and X-Hunters. With the aid of a new Zero and capsules from Dr. Light, X was able to destroy the new Sigma that was behind the Second War.

After the war, a reploid doctor called Dr. Doppler was able to discover a 'Sigma Virus' that was responsible for turning reploids into Mavericks. He was able to develop an anti-virus and soon he was able to develop a utopia he called 'Doppler Town'. However, the utopia ended before it was started. Doppler had turned Doppler Town into a new Maverick base, and he was leading a new revolt, the Third Maverick War. The anti-virus was a placebo. Doppler's first attack was made on the Maverick Hunter base. X and Zero were able to clear out the area, but the war was far from over. With the help of Zero and new capsules from Dr. Light, X was able to infiltrate Doppler Town and was able to destroy Dr. Doppler. However, Dr. Cain discovered that Doppler was developing a new battle body. This was for the new Sigma that Doppler was able to restore. X had to destroy Sigma once again.

Peace returned for a while, but the peace was broken when Mavericks attacked the air city Sky Lagoon, and it appeared to be Repliforce. This was the start of the Fourth Maverick War, or Repliforce's War for Independence. Repliforce was unrightfully called Mavericks, which sparked their desire for independence. The 8 new forces consisted of 5 Repliforce commanders and three Mavericks, one of which was Magma Dragoon, ex-leader of the 14th Unit. X and Zero were able to stop the 8 reploids and discovered that Repliforce had gone into outer space. X and Zero were able to defeat General, the leader of Repliforce, but some other force was controlling the weapon that Repliforce developed. X and Zero soon discovered that Sigma had somehow came back and was controlling the weapon. Even though X and Zero were able to destroy the four forms of Sigma, the weapon was aimed at Earth with no apparent way of stopping it. General was able to destroy the weapon, but he was destroyed with it.