Contrary to popular belief, Mega Man X is the second version of Mega Man created by Dr. Light.
(In case you didn't know, Mega Man died at the hands of Zero.)
Enhanced with new armor as well as the ability to make his own choices, he now commands the Maverick Hunters.

Mega Man X is an upgraded version of Mega Man. He was Doctor Light's final creation before his passing.
He is best friends with Zero, the last creation of Dr. Wily. Zero was named for the number of people that would be alive when he carried out his programming.
Dr. Cain discovered Mega Man X and was amazed at how advanced he was, being able to really think for himself and experience emotions.
Soon, Dr. Cain began creating Replodis, or robots built to the tune of X and his ability to experience emotion.
His most powerful creation was Sigma. Sigma was built when more and more Reploids became Maverick, or dangerous to humans. He headed up the Maverick Hunters, a group of Reploids dedicated to hunt down Mavericks.
One day, Sigma and Zero engaged in a great battle deep in a cave. However, during the climax of the battle, a virus which was implanted in Zero transfered itself in entirety, along with memories Zero had, to Sigma. Sigma won the battle and ordered Zero taken back to headquarters to be repaired, but Sigma disappeared. He would reappear later as X and Zero's greatest rival and biggest threat.
Zero was repaired and became the new leader of the Maverick Hunters. During a particuarly bad outbreak of Maverick activity, X decided that he was not doing enough to help. He set off and at the end of his first mission fought Vile in his ride armor, who easy defeated X in battle. However, before Vile could destroy X, Zero stepped in and saved X.
After X defeated the Mave...

The greatest videogame franchise ever!

While the details are unknown as of yet (Damn Capcom always starting a spin-off before finishing the original), it is assumed that Mega Man X, or simply X, was an upgraded version of Mega Man, a service robot remodeled for war. Dr. Light, who created Mega Man, programed X to give Mega Man the gift of free will. Before he released X, he put him in a stasis capsle for 30 years to run tests to determine that X wouldn't breat any of the laws of robotics. 30 years later, X was found and reactivated by Dr. Cain. Robots were built based off of X's programing called Reploids. Everything seemed to be fine until a renegade Reploid harmed a Human. A Reploid who does that is called a Maverick. This robot was quickly destroyed, but soon other reploids went Maverick, and a Maverick Hunter force had to be assembled which was led by Dr. Cain's own best robot, Sigma. Unfortunately Sigma too went Maverick and X once again had to give up a life of peace to save the human race along with another Hunter, Zero.