The story begins three weeks after Mega Man X5, with Zero missing, presumed dead, and the Earth's surface rendered uninhabitable. When he was revived, he panicked upon seeing X and Zero, but then decided to challenge them for their DNA data. Gate didn't seem to care that he was disposed of, but revived him as part of his investigation team. Gate then sent Scaravich to a forbidden area, where Alia promptly disposed of him as punishment. Gate, interested in the data, took care of Scaravich in exchange for it. Ground Scaravich - Scaravich was a treasure hunter bent on researching ancient data.When Gate revived him, he took his place back in the Recycle Lab and continued to work on projects.

However, DNA resurrection was strictly prohibited by law and he was dealt with swiftly. Gate, also interested in this, encouraged him. However, he was interested in DNA data and used it to revive felled Mavericks.

Metal Shark Player - Metal Shark Player once worked for the recycling team and was eventually put in charge of the Recycle Lab.

X and Zero disposed of him when he challenged them. He seemed arrogant at first, but later turned to rage when he realized that his creation had been destroyed. They destroyed the robot, and then met with Mijinion. When X and Zero arrived, Illumina was active, but still in its testing phases. When he was revived by Gate, he took hold of the Weapon Center and constructed a giant war machine known as Illumina. The Reploid Research team destroyed him and made it look like an accident. Though he always produced excellent results, he was brash in his decision making and didn't get along with his co-workers.

Infinity Mijinion - Mijinion was a fiesty weapon tester.

When Gate revived him, he occupied the Magma Area and was destroyed once again by X and Zero. However, all those who fell behind in his party were murdered by him, and therefore he was disposed of by the Reploid Research Team.

Blaze Heatnix - Blaze was part of an investigation team and constructed specifically to handle hot areas.

When he was revived by Gate, he insisted on using the second chance to complete his mission. The Reploid Research Team tricked Alia into killing Wolfang by throwing him into the sea. He managed to fend them off, but his team members were killed.

Blizzard Wolfang - Wolfang was an investigator in the North Pole area, and his team was one day attacked by Mavericks.

He was then revived by Gate, swearing to protect him no matter what. Unable to handle being labeled as such, he took his own life. He was then labeled a Maverick by association. Jim went Maverick and had to be destroyed, and Shield blamed himself for not protecting him from coming under the virus' influence.

Shield Sheldon - Shield was a rookie bodyguard assigned to protect the famous Dr.

When Gate revived him, he once again layed down his life, this time for the Maverick Hunters, in order to defend his master. Gate was to be punished for this, but Rainy Turtloid gave his life to save him. Rainy Turtloid was very loyal to Gate, trusting everything he said and did. Requests to weaken him grew, but Gate opposed it. However, his defensive power frightened other Reploids, especially given that his creator was known to make Reploids that were unanalyzable and sometimes erratic. Due to his high protective ability, he could investigate areas not possible by any other Reploid.

Rainy Turtloid - Rainy Turtloid was created by Gate to investigate polluted areas.

When he was revived by Gate, he felt he could trust no one and challenged X and Zero as a means to his own survival. He was never officially accused of the incident, but the Reploid Research team disposed of him by altering his flying system. Unable to control his system, though, he accidentally burned down the forest he was meant to protect.

Commander Yammark - Yammark was built as part of a project to help preserve nature.

High Max - A powerful Reploid created by Gate, supposedly built to investigate the Nightmare virus alongside his fellow investigators.

Isoc - Gate's mysterious assistant, obsessed with finding Zero, even goes so far as to claim that he knows everything about him.

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