X is constantly having conflicts with his own artificial conscience. Built to rid the world of evil forces, he carries on his duties as faithfully as possible. Unfortunately, he despises war and the concept of it, and wonders what will become of him in the future. Unlike his friend, Zero, who has his thoughts sorted through, X may appear with several different character sets, due to the heavy responsibility placed upon his shoulders.
In the end, X fears that his instability of mind and the pressure of his occupation may cause him to become a Maverick.
It is interesting to note that, while responsible for awakening and assisting X, his invention of Reploids was the direct cause of all the major wars throughout the X, Zero, and ZX games, resulting in rapid, dramatic changes of society that are often for the worst. In this spirit, it is also interesting to note that his original background was in archaeology. Some speculated that his seeming unfamiliarity with robotics at the outset of the X series could have accounted for at least some of the problems that arose after his creation of Reploid-kind, but the discovery that the Maverick condition was caused by a computer virus laid many of these ideas to rest.
Iris was developed by Repliforce scientists as half of the perfect fighting Reploid. Colonel, her brother, was the other half. Her half was of the peaceful arbitrator, and Colonel's was of the strong-willed fighter. Repliforce scientists had struggled to make these two factors into one Reploid, but the differences were irreconcilable, so they split them into brother and sister Reploids.
Iris trained with the Maverick Hunters, and during this time she developed feelings for Zero. Later, Zero saved her during the Sky Lagoon incident, and she acted as a navigator at the Maverick Hunter Headquearters, instructing Zero on where to go for his missions. Despite her willingness to instruct Zero, she constantly urged him to withhold his fighting, especially from her brother. When they faced off, she stopped the fight before anyone could get hurt. But to her dismay, Zero was only spurred on further to stop the Repliforce.
When her brother was later destroyed at the hands of Zero, the pain drove Iris mad and she made a trip to the Final Weapon. She waited for Zero in a laboratory ready to avenge her brother, where she used Colonel's fighting will to gain a powerful body armor. Like the Repliforce scientists had discovered, her system wouldn't accept the fighting spirit and frequently rejected it as she fought, causing her horrible pain. Zero defeated her, but rushed to her side instantly after; it was too late at this point, as Iris was already dying. It was at this point that she admitted point-blank that she had feelings for Zero, admitting that the utopia was a myth, but claiming she wanted to be there with Zero.
Iris makes a small cameo in Mega Man X5, when using Zero to destroy Sigma's latest incarnation. Zero remembers her while reflecting on his life as he himself perishes due to most of his body being destroyed. She also appeared as X's and Zero's guide in Mega Man Xtreme 2 for the Game Boy Color, which does follow the X series characters. This game takes place before the events of Mega Man X4.
An alternate universe version of her appears in the last installment of the Battle Network series, Mega Man Battle Network 6, and plays a significant role in the storyline.
Alia began her career as a simple researcher in Reploid engineering. She and her colleague Gate were ahead of their time in their research on Reploids, though she contends that Gate was always a better programmer than she was. However, Gate's inability to follow the rules made him a social outcast, and his creations were systematically destroyed, sometimes even with the assistance of Alia herself. She soon mastered all programming languages and was chosen on these merits to be a spotter for the Hunters. In Mega Man X5, Alia then served as the Hunters' spotter (navigator) during the Sigma Virus outbreak, while simultaneously lending her technical talents to the cause by uploading and letting X utilize his two new armors, the Falcon and Gaea armor. She supported the Hunters throughout the ordeal until it was resolved.
In Mega Man X6, she spotted X and Zero as they dealt with the Nightmares, and her past with Gate came back to haunt her. Though feeling guilty throughout the happenings, she assisted the Hunters in bringing Gate to justice. When Gate was defeated, though, X brought his remains to Alia, and she said she would do her best to repair him, although it's unknown if she ever succeeded or not. As the Earth Recovery proceeded, Alia continued to act as a Hunter navigator. Her skills were brought to good use when Axl escaped from the Red Alert Syndicate, a new hunter organization that had risen to power, in the Mega Man X7 installment. With X having retired from the Hunters, he assisted Alia with her work at the base. During the crisis, Alia continued to guide Zero and Axl - and X, once he decided that he needed to help out - on their missions, eventually helping them locate Red Alert's base.
In Mega Man X8, Alia continued her spotter position, assisted by two new navigators (Layer and Palette). Working in tandem, she assists in the discovery of the new generation chips and Sigma's plot. Alia is also a secret unlockable character in the game and is similar to X in terms of controls.
Axl is introduced in Mega Man X7, having just left the mercenary Red Alert Syndicate and seeking asylum and membership in the Maverick Hunters. The Red Alert Syndicate, which hunts Mavericks and also takes on less savory assassination jobs, has been infiltrated by Sigma, and confronts the Maverick Hunters. X, Zero, and Axl work together to defeat Red Alert, but in so doing, destroy both Red, the leader of Red Alert, and Sigma, the only ones Axl knows of who know about his origins. He has a very special ability called Copy Shot, which allows him to disguise himself as certain non-boss enemies with A-Trans, the enfusing of the enemy's DNA data. In Mega Man X: Command Mission, Redips, initially the leader of the maverick hunters, also has the ability to transform. In MMX:CM, Axl's Action Trigger allows him to turn into defeated bosses such as Wild Jango, Silver Horn, Mad Nautilus, Mach Jentra, Incentas, Depth Dragoon, Rafflesian and Ninetails. His Hyper Mode, Stealth Mode, allows him to avoid enemy attacks, similar to that of Spiders Hyper Mode, Trickstar.
Mega Man X8 reveals that Axl is a prototype for a next-generation reploid. These next-generation reploids all have the ability to copy other reploids, as well as a chip that prevents them from going Maverick. These next-generation reploids are pawns in two different plots:
X, Zero, and Axl defeat them both, but when Lumine is defeated, he lashes out in his death throes, cracking the crystal on Axl's head.
Although the Biometal Model A appearing in Mega Man ZX Advent is heavily implied to be based on Axl, using twin pistols and carrying the A Trans ability, it is instead based on Master Albert, which creates some speculation about Master Albert's origins. Model A is voiced by Yu Kobayashi.
After this, he reappears in a handful of later games, having been reactivated in the latest plot. In Mega Man X3, Vile is rebuilt by the rogue Dr. Doppler, and in Mega Man Xtreme, Vile is revived in digital form by Techno. Both times, he is defeated by X. He has a somewhat larger role in Mega Man X8, where he attacks the protagonists multiple times on behalf of Sigma and Lumine.
Vile is a playable character in Mega Man Maverick Hunter X, and in his version of the single-player story he is recast as a loose cannon who is freed from imprisonment by Sigma to wreak havoc (his change of allegiance is reflected in his appearance; unlike in the original Mega Man X, the symbol on his forehead is a V instead of Sigma's stylized Σ). He turns against Sigma's Mavericks, but in his final battle, instead of fighting Sigma, he confronts both X and Zero, though he ends up being destroyed in the end.
He made a one-episode appearance in the 1994 Mega Man cartoon by Ruby-Spears alongside X and Spark Mandrill. In this appearance, he was surprisingly similar to his game's counterpart in terms of appearance, when compared to many of the other characters. The addition of a neck and a taller, slightly more detailed head are the main differences, although it should also be noted that whenever he is about to attack, he grabs his shoulder cannon and aims manually, unlike the games (with the exception of his Maverick Hunter X ending, which came out years after the cartoon was made). Mega Man didn't stand a chance against Vile because the shots from his arm cannon were just deflected off of Vile's ride armor. His personality is vastly different; in the games he is relatively crazy, possibly psychotic, but in the cartoon he is a collected character and has a deep, calm voice. He's very arrogant, often calling Mega Man "puny", and when he hears Dr. Wily come up with what he views a good plan, Vile says "not bad, for a puny human". His actual objective was to steal the lightanium rods developed by Dr. Light, which according to X were worth billions in the future, and which Sigma planned to use them to fund his war against the humans. Vile is also heavily implied to have a grudge against X.
Over time, the Maverick Virus has apparently fused with his mind, making the virus and Sigma the same entity. This is how Sigma keeps surviving his defeats at the end of each game. Sigma has a habit of fighting first in his normal body, which the player must destroy, and then switching over to a much more powerful body that is hidden in the background. As such, the term "pulling a Sigma" is sometimes used as video game jargon to describe someone who is defeated and then comes back a moment later fully healed and more powerful than they were before through unknown means.
The ending of Mega Man X8 seems to indicate that Sigma has finally been defeated for good and will not return, due to the fact that his viral form was released on the Moon, where it has very little chance of corrupting anyone else. According to the Mega Man Zero storyline, it is possible that the Sigma Virus just lingered on the moon for a period of time before finally being deleted by the Mother Elf (this may prove to be true, as Sigma's viral form can survive in space, as shown in the fact that even though he was killed on Repliforce's Final Weapon in Mega Man X4 in the middle of space, he fully returns for the events of X5).
Dynamo was hired by Sigma to help his execution of the plan to spread the Maverick virus all over Earth. Once Sigma had executed the plan, Dynamo's job was to slow down the progress of X and Zero as they gathered parts for the Enigma cannon and the Shuttle, both of which were intended to stop the colony's crash, which was an integral part of Sigma's plan. Despite his arrogant claims, he escaped in a fit of cowardice when X and Zero defeated him, bringing him to the realization that he could die. This showed that he was still intelligent and hasn't turned Maverick, as most Mavericks would refuse to back down and fight till their destruction. With Sigma no longer around to protect him during Mega Man X6, he attempted gathering Nightmare Souls to enhance his power. However, he still failed miserably at fighting X and Zero, and escaped from them again. For unknown reasons, he has made no subsequent appearances after X6.
In X5, Dynamo is somewhat notable as the only boss other than the eight Mavericks that gets his own intro sequence.